The data consists of vegetation % cover by functional group from across CONUS (from AIM, FIA, LANDFIRE, and RAP), as well as climate variables from DayMet, which have been aggregated into mean interannual conditions accross multiple temporal windows.

Dependencies

Set user defined parameters

print(params)
## $autoKfold
## [1] FALSE
## 
## $run
## [1] TRUE
## 
## $save_figs
## [1] FALSE
## 
## $trimAnomalies
## [1] TRUE
## 
## $ecoregion
## [1] "forest"
## 
## $response
## [1] "TotalTreeCover"
## 
## $removeTexasLouisianaPlain
## [1] FALSE
# set to true if want to run for a limited number of rows (i.e. for code testing)
test_run <- params$test_run
save_figs <- params$save_figs
response <- params$response
fit_sample <- TRUE # fit model to a sample of the data
n_train <- 5e4 # sample size of the training data
n_test <- 1e6 # sample size of the testing data (if this is too big the decile dotplot code throws memory errors)
trimAnom <- params$trimAnomalies
removeTLP <- params$removeTexasLouisianaPlain
run <- params$run
autoKfold <- params$autoKfold

Load packages and source functions

# set option so resampled dataset created here reproduces earlier runs of this code with dplyr 1.0.10
source("../../../Functions/glmTransformsIterates.R")
source("../../../Functions/transformPreds.R")
source("../../../Functions/betaLASSO.R")

#source("../../../Functions/StepBeta_mine.R")
#source("src/fig_params.R")
#source("src/modeling_functions.R")
 
library(betareg)
library(ggspatial)
library(terra)
library(tidyterra)
library(sf)
library(caret)
library(tidyverse)
library(GGally) # for ggpairs()
library(pdp) # for partial dependence plots
library(gridExtra)
library(knitr)
library(patchwork) # for figure insets etc. 
library(ggtext)
library(StepBeta)
theme_set(theme_classic())
library(here)
library(rsample)
library(kableExtra)
library(glmnet)
library(USA.state.boundaries)

Read in data

Data compiled in the prepDataForModels.R script

here::i_am("Analysis/VegComposition/ModelFitting/02_ModelFitting.Rmd")
modDat <- readRDS( here("Data_processed", "CoverData", "DataForModels_spatiallyAveraged_withSoils_noSf.rds"))

# change Level 1 cover variables to be between 0 and 1 rather than 0 and 100
modDat[,"TotalTreeCover"] <- modDat[,"TotalTreeCover"]/100
modDat[,"TotalHerbaceousCover"] <- modDat[,"TotalHerbaceousCover"]/100
modDat[,"BareGroundCover"] <- modDat[,"BareGroundCover"]/100
modDat[,"ShrubCover"] <- modDat[,"ShrubCover"]/100

# For all response variables, make sure there are no 0s add  .0001 from each, since the Beta model framework can't handle that
modDat[modDat$TotalTreeCover == 0 & !is.na(modDat$TotalTreeCover), "TotalTreeCover"] <- 0.0001
modDat[modDat$TotalHerbaceousCover == 0  & !is.na(modDat$TotalHerbaceousCover), "TotalHerbaceousCover"] <- 0.0001
modDat[modDat$BareGroundCover == 0 & !is.na(modDat$BareGroundCover), "BareGroundCover"] <- 0.0001
modDat[modDat$ShrubCover == 0 & !is.na(modDat$ShrubCover), "ShrubCover"] <- 0.0001
#change 0s to .000001 so model will run
modDat[modDat$AngioTreeCover_prop == 0 & !is.na(modDat$AngioTreeCover_prop), "AngioTreeCover_prop"] <- 0.0001
modDat[modDat$ConifTreeCover_prop == 0 & !is.na(modDat$ConifTreeCover_prop), "ConifTreeCover_prop"] <- 0.0001
modDat[modDat$C4GramCover_prop == 0 & !is.na(modDat$C4GramCover_prop), "C4GramCover_prop"] <- 0.0001
modDat[modDat$C3GramCover_prop == 0 & !is.na(modDat$C3GramCover_prop), "C3GramCover_prop"] <- 0.0001
modDat[modDat$ForbCover_prop == 0 & !is.na(modDat$ForbCover_prop), "ForbCover_prop"] <- 0.0001

# For all response variables, make sure there are no values of 1 -- subtract .0001 from each, since the Beta model framework can't handle that
modDat[modDat$TotalTreeCover == 1 & !is.na(modDat$TotalTreeCover), "TotalTreeCover"] <- 0.9999
modDat[modDat$TotalHerbaceousCover == 1  & !is.na(modDat$TotalHerbaceousCover), "TotalHerbaceousCover"] <- 0.9999
modDat[modDat$BareGroundCover == 1 & !is.na(modDat$BareGroundCover), "BareGroundCover"] <- 0.9999
modDat[modDat$ShrubCover == 1 & !is.na(modDat$ShrubCover), "ShrubCover"] <- 0.9999
#change 0s to .000001 so model will run
modDat[modDat$AngioTreeCover_prop == 1 & !is.na(modDat$AngioTreeCover_prop), "AngioTreeCover_prop"] <- 0.9999
modDat[modDat$ConifTreeCover_prop == 1 & !is.na(modDat$ConifTreeCover_prop), "ConifTreeCover_prop"] <- 0.9999
modDat[modDat$C4GramCover_prop == 1 & !is.na(modDat$C4GramCover_prop), "C4GramCover_prop"] <- 0.9999
modDat[modDat$C3GramCover_prop == 1 & !is.na(modDat$C3GramCover_prop), "C3GramCover_prop"] <- 0.9999
modDat[modDat$ForbCover_prop == 1 & !is.na(modDat$ForbCover_prop), "ForbCover_prop"] <- 0.9999

Prep data

set.seed(1234)
modDat_1 <- modDat %>% 
  dplyr::select(-c(prcp_annTotal:annVPD_min)) %>% 
  # mutate(Lon = st_coordinates(.)[,1], 
  #        Lat = st_coordinates(.)[,2])  %>% 
  # st_drop_geometry() %>% 
  # filter(!is.na(newRegion))
  rename("tmin" = tmin_meanAnnAvg_CLIM, 
     "tmax" = tmax_meanAnnAvg_CLIM, #1
     "tmean" = tmean_meanAnnAvg_CLIM, 
     "prcp" = prcp_meanAnnTotal_CLIM, 
     "t_warm" = T_warmestMonth_meanAnnAvg_CLIM,
     "t_cold" = T_coldestMonth_meanAnnAvg_CLIM, 
     "prcp_wet" = precip_wettestMonth_meanAnnAvg_CLIM,
     "prcp_dry" = precip_driestMonth_meanAnnAvg_CLIM, 
     "prcp_seasonality" = precip_Seasonality_meanAnnAvg_CLIM, #2
     "prcpTempCorr" = PrecipTempCorr_meanAnnAvg_CLIM,  #3
     "abvFreezingMonth" = aboveFreezing_month_meanAnnAvg_CLIM, 
     "isothermality" = isothermality_meanAnnAvg_CLIM, #4
     "annWatDef" = annWaterDeficit_meanAnnAvg_CLIM, 
     "annWetDegDays" = annWetDegDays_meanAnnAvg_CLIM,
     "VPD_mean" = annVPD_mean_meanAnnAvg_CLIM, 
     "VPD_max" = annVPD_max_meanAnnAvg_CLIM, #5
     "VPD_min" = annVPD_min_meanAnnAvg_CLIM, #6
     "VPD_max_95" = annVPD_max_95percentile_CLIM, 
     "annWatDef_95" = annWaterDeficit_95percentile_CLIM, 
     "annWetDegDays_5" = annWetDegDays_5percentile_CLIM, 
     "frostFreeDays_5" = durationFrostFreeDays_5percentile_CLIM, 
     "frostFreeDays" = durationFrostFreeDays_meanAnnAvg_CLIM, 
     "soilDepth" = soilDepth, #7
     "clay" = surfaceClay_perc, 
     "sand" = avgSandPerc_acrossDepth, #8
     "coarse" = avgCoarsePerc_acrossDepth, #9
     "carbon" = avgOrganicCarbonPerc_0_3cm, #10
     "AWHC" = totalAvailableWaterHoldingCapacity,
     ## anomaly variables
     tmean_anom = tmean_meanAnnAvg_3yrAnom, #15
     tmin_anom = tmin_meanAnnAvg_3yrAnom, #16
     tmax_anom = tmax_meanAnnAvg_3yrAnom, #17
    prcp_anom = prcp_meanAnnTotal_3yrAnom, #18
      t_warm_anom = T_warmestMonth_meanAnnAvg_3yrAnom,  #19
     t_cold_anom = T_coldestMonth_meanAnnAvg_3yrAnom, #20
      prcp_wet_anom = precip_wettestMonth_meanAnnAvg_3yrAnom, #21
      precp_dry_anom = precip_driestMonth_meanAnnAvg_3yrAnom,  #22
    prcp_seasonality_anom = precip_Seasonality_meanAnnAvg_3yrAnom, #23 
     prcpTempCorr_anom = PrecipTempCorr_meanAnnAvg_3yrAnom, #24
      aboveFreezingMonth_anom = aboveFreezing_month_meanAnnAvg_3yrAnom, #25  
    isothermality_anom = isothermality_meanAnnAvg_3yrAnom, #26
       annWatDef_anom = annWaterDeficit_meanAnnAvg_3yrAnom, #27
     annWetDegDays_anom = annWetDegDays_meanAnnAvg_3yrAnom,  #28
      VPD_mean_anom = annVPD_mean_meanAnnAvg_3yrAnom, #29
      VPD_min_anom = annVPD_min_meanAnnAvg_3yrAnom,  #30
      VPD_max_anom = annVPD_max_meanAnnAvg_3yrAnom,  #31
     VPD_max_95_anom = annVPD_max_95percentile_3yrAnom, #32
      annWatDef_95_anom = annWaterDeficit_95percentile_3yrAnom, #33 
      annWetDegDays_5_anom = annWetDegDays_5percentile_3yrAnom ,  #34
    frostFreeDays_5_anom = durationFrostFreeDays_5percentile_3yrAnom, #35 
      frostFreeDays_anom = durationFrostFreeDays_meanAnnAvg_3yrAnom #36
  ) %>% 
  dplyr::select(-c(tmin_meanAnnAvg_3yr:durationFrostFreeDays_meanAnnAvg_3yr))
## Add a constant to the response variable (+2) so that models run...
# but we're not doing that this time...
modDat_1 <- modDat_1 %>% 
mutate(response_transformed = .[[response]] + 0)#+ 2) 
names(modDat_1)[names(modDat_1) == "response_transformed"] <- paste0(response, "_transformed")

Identify the ecoregion and response variable type to use in this model run

ecoregion <- params$ecoregion
response <- params$response
print(paste0("In this model run, the ecoregion is ", ecoregion," and the response variable is ",response))
## [1] "In this model run, the ecoregion is forest and the response variable is TotalTreeCover"

Visualize the predictor variables

The following are the candidate predictor variables for this ecoregion:

if (ecoregion == "shrubGrass") {
  # select potential predictor variables for the ecoregion of interest
        prednames <-
          c(
"tmean"             , "prcp"                    ,"prcp_seasonality"        ,"prcpTempCorr"          , 
"isothermality"     , "annWatDef"               ,"sand"                    ,"coarse"                , 
"carbon"            , "AWHC"                    ,"tmin_anom"               ,"tmax_anom"             , 
"t_warm_anom"       , "prcp_wet_anom"           ,"precp_dry_anom"          ,"prcp_seasonality_anom" , 
"prcpTempCorr_anom" , "aboveFreezingMonth_anom" ,"isothermality_anom"      ,"annWatDef_anom"        , 
"annWetDegDays_anom", "VPD_mean_anom"           ,"VPD_min_anom"            ,"frostFreeDays_5_anom"   )
  
} else if (ecoregion %in% c("forest", "eastForest", "westForest")) {
  # select potential predictor variables for the ecoregion of interest
  prednames <- 
    c(
"tmean"                 ,"prcp"               , "prcp_dry"                , "prcpTempCorr"      ,     
"isothermality"         ,"annWatDef"          , "clay"                    , "sand"              ,     
"coarse"                ,"carbon"             , "AWHC"                    , "tmin_anom"         ,     
"tmax_anom"             ,"prcp_anom"          , "prcp_wet_anom"           , "precp_dry_anom"    ,     
"prcp_seasonality_anom" ,"prcpTempCorr_anom"  , "aboveFreezingMonth_anom" , "isothermality_anom",     
"annWatDef_anom"        ,"annWetDegDays_anom" , "VPD_mean_anom"           , "VPD_max_95_anom"   ,     
"frostFreeDays_5_anom"   )
} else if (ecoregion == "CONUS") {
  prednames <- c(
    "tmean"               ,"prcp"               ,"prcp_seasonality", "prcpTempCorr"       ,  "isothermality"     ,     
"annWetDegDays"           ,"sand"               ,"coarse"         , "AWHC"                , "tmin_anom"          ,    
"tmax_anom"               ,"prcp_wet_anom"      ,"precp_dry_anom" , "prcp_seasonality_anom", "prcpTempCorr_anom" ,     
"aboveFreezingMonth_anom" ,"isothermality_anom" ,"annWatDef_anom" , "annWetDegDays_anom"  , "VPD_mean_anom"      ,    
"VPD_max_95_anom"         ,"frostFreeDays_5_anom"   
  )
} 

# get the name of the transformed response
response_t <- paste0(response, "_transformed")

Scale the predictor variables for the model-fitting process

allPreds <- modDat_1 %>% 
  dplyr::select(tmin:frostFreeDays,tmean_anom:frostFreeDays_anom, soilDepth:AWHC) %>% 
  names()
modDat_1_s <- modDat_1 %>% 
  mutate(across(all_of(allPreds), base::scale, .names = "{.col}_s")) 
saveRDS(modDat_1_s, file = "./models/scaledModelInputData.rds")

Subset the data to only include data for the ecoregion of interest

if (ecoregion == "shrubGrass") {
  # select data for the ecoregion of interest
  modDat_1_s <- modDat_1_s %>%
    filter(newRegion == "dryShrubGrass")
} else if (ecoregion == "forest") {
  # select data for the ecoregion of interest
  modDat_1_s <- modDat_1_s %>% 
    filter(newRegion %in% c("eastForest", "westForest"))
} else if (ecoregion == "CONUS") {
  modDat_1_s <- modDat_1_s
} else if (ecoregion == "eastForest") {
   modDat_1_s <- modDat_1_s %>% 
    filter(newRegion == "eastForest")
} else if (ecoregion == "westForest") {
    modDat_1_s <- modDat_1_s %>% 
    filter(newRegion == "westForest")
}
# remove the rows that have no observations for the response variable of interest
modDat_1_s <- modDat_1_s[!is.na(modDat_1_s[,response]),]
# subset the data to only include these predictors, and remove any remaining NAs 
modDat_1_s <- modDat_1_s %>% 
  dplyr::select(prednames, paste0(prednames, "_s"), response, response_t, newRegion, Year, Long, Lat, NA_L1NAME, NA_L2NAME) %>% 
  drop_na()

names(prednames) <- prednames
df_pred <- modDat_1_s[, prednames]

Visualize the response variable

hist(modDat_1_s[,response], main = paste0("Histogram of ",response),
     xlab = paste0(response))

create_summary <- function(df) {
  df %>% 
    pivot_longer(cols = everything(),
                 names_to = 'variable') %>% 
    group_by(variable) %>% 
    summarise(across(value, .fns = list(mean = ~mean(.x, na.rm = TRUE), min = ~min(.x, na.rm = TRUE), 
                                        median = ~median(.x, na.rm = TRUE), max = ~max(.x, na.rm = TRUE)))) %>% 
    mutate(across(where(is.numeric), round, 4))
}

modDat_1_s[prednames] %>% 
  create_summary() %>% 
  knitr::kable(caption = 'summaries of possible predictor variables') %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed")) 
summaries of possible predictor variables
variable value_mean value_min value_median value_max
AWHC 12.9843 0.9085 12.2930 34.6680
VPD_max_95_anom 0.0141 -0.4911 0.0062 0.6820
VPD_mean_anom -0.0415 -0.3682 -0.0408 0.1425
aboveFreezingMonth_anom 0.1472 -1.7727 0.1000 2.8241
annWatDef 44.8060 0.0000 36.2688 308.3581
annWatDef_anom -0.1447 -6.7483 -0.1476 1.0000
annWetDegDays_anom -0.0007 -0.9415 -0.0051 0.6927
carbon 9.1928 0.2171 6.1178 48.1381
clay 17.2232 0.0286 16.8115 83.0975
coarse 18.7825 0.0000 17.7685 64.1122
frostFreeDays_5_anom -27.9495 -289.5000 -30.0000 51.8500
isothermality 37.6093 21.4503 37.6660 60.8054
isothermality_anom 0.7789 -6.9716 0.7887 10.8130
prcp 1071.2525 214.0058 889.1041 4360.3490
prcpTempCorr -0.3060 -0.8613 -0.3604 0.7098
prcpTempCorr_anom -0.0014 -0.5313 0.0088 0.5459
prcp_anom 0.0207 -0.6527 0.0201 0.5567
prcp_dry 11.0499 0.0000 6.5744 81.8916
prcp_seasonality_anom -0.0207 -0.5679 -0.0118 0.4421
prcp_wet_anom 0.0097 -1.2034 0.0168 0.6194
precp_dry_anom 0.1321 -6.7500 0.1766 1.0000
sand 45.7208 0.0098 45.3002 99.9418
tmax_anom -0.3340 -4.8736 -0.3265 3.9384
tmean 7.9682 -2.3375 7.1464 24.1827
tmin_anom -0.7327 -5.3609 -0.6615 1.8934

Histograms of raw and scaled predictors

scaleFigDat_1 <- modDat_1_s %>% 
  dplyr::select(c(Long, Lat, Year, prednames)) %>% 
  pivot_longer(cols = all_of(names(prednames)), 
               names_to = "predNames", 
               values_to = "predValues_unScaled")
scaleFigDat_2 <- modDat_1_s %>% 
  dplyr::select(c(Long, Lat, Year, paste0(prednames, "_s"))) %>% 
  pivot_longer(cols = all_of(paste0(prednames,"_s"
                                    )), 
               names_to = "predNames", 
               values_to = "predValues_scaled", 
               names_sep = ) %>% 
  mutate(predNames = str_replace(predNames, pattern = "_s$", replacement = ""))

scaleFigDat_3 <- scaleFigDat_1 %>% 
  left_join(scaleFigDat_2)

ggplot(scaleFigDat_3) + 
  facet_wrap(~predNames, scales = "free") +
  geom_histogram(aes(predValues_unScaled), fill = "lightgrey", col = "darkgrey") + 
  geom_histogram(aes(predValues_scaled), fill = "lightblue", col = "blue") +
  xlab ("predictor variable values") + 
  ggtitle("Comparing the distribution of unscaled (grey) to scaled (blue) predictor variables")

modDat_1_s <- modDat_1_s %>% 
  rename_with(~paste0(.x, "_raw"), 
                any_of(names(prednames))) %>% 
  rename_with(~str_remove(.x, "_s$"), 
              any_of(paste0(names(prednames), "_s")))

Predictor variables compared to binned response variables

set.seed(12011993)
# vector of name of response variables
vars_response <- response
# longformat dataframes for making boxplots
df_sample_plots <-  modDat_1_s  %>% 
  slice_sample(n = 5e4) %>% 
   rename(response = all_of(response_t)) %>% 
  mutate(response = case_when(
    response <= .25 ~ ".25", 
    response > .25 & response <=.50 ~ ".50", 
    response > .50 & response <=.75 ~ ".75", 
    response >= .75  ~ "1", 
  )) %>% 
  dplyr::select(c(response, prednames)) %>% 
  tidyr::pivot_longer(cols = unname(prednames), 
               names_to = "predictor", 
               values_to = "value"
               )  
 

  ggplot(df_sample_plots, aes_string(x= "response", y = 'value')) +
  geom_boxplot() +
  facet_wrap(~predictor , scales = 'free_y') + 
  ylab("Predictor Variable Values") + 
    xlab(response)

Model Fitting

Visualize the spatial blocks and how they differ across environmental space

First, if there are observations in Louisiana, sub-sample them so they’re not so over-represented in the dataset

## make data into spatial format
modDat_1_sf <- modDat_1_s %>% 
  st_as_sf(coords = c("Long", "Lat"), crs = st_crs("PROJCRS[\"unnamed\",\n    BASEGEOGCRS[\"unknown\",\n        DATUM[\"unknown\",\n            ELLIPSOID[\"Spheroid\",6378137,298.257223563,\n                LENGTHUNIT[\"metre\",1,\n                    ID[\"EPSG\",9001]]]],\n        PRIMEM[\"Greenwich\",0,\n            ANGLEUNIT[\"degree\",0.0174532925199433,\n                ID[\"EPSG\",9122]]]],\n    CONVERSION[\"Lambert Conic Conformal (2SP)\",\n        METHOD[\"Lambert Conic Conformal (2SP)\",\n            ID[\"EPSG\",9802]],\n        PARAMETER[\"Latitude of false origin\",42.5,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8821]],\n        PARAMETER[\"Longitude of false origin\",-100,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8822]],\n        PARAMETER[\"Latitude of 1st standard parallel\",25,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8823]],\n        PARAMETER[\"Latitude of 2nd standard parallel\",60,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8824]],\n        PARAMETER[\"Easting at false origin\",0,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8826]],\n        PARAMETER[\"Northing at false origin\",0,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8827]]],\n    CS[Cartesian,2],\n        AXIS[\"easting\",east,\n            ORDER[1],\n            LENGTHUNIT[\"metre\",1,\n                ID[\"EPSG\",9001]]],\n        AXIS[\"northing\",north,\n            ORDER[2],\n            LENGTHUNIT[\"metre\",1,\n                ID[\"EPSG\",9001]]]]"))


# download map info for visualization
data(state_boundaries_wgs84) 

cropped_states <- suppressMessages(state_boundaries_wgs84 %>%
  dplyr::filter(NAME!="Hawaii") %>%
  dplyr::filter(NAME!="Alaska") %>%
  dplyr::filter(NAME!="Puerto Rico") %>%
  dplyr::filter(NAME!="American Samoa") %>%
  dplyr::filter(NAME!="Guam") %>%
  dplyr::filter(NAME!="Commonwealth of the Northern Mariana Islands") %>%
  dplyr::filter(NAME!="United States Virgin Islands") %>%
  sf::st_sf() %>%
  sf::st_transform(sf::st_crs(modDat_1_sf))) #%>%
  #sf::st_crop(sf::st_bbox(modDat_1_sf)+c(-1,-1,1,1))
if (ecoregion %in% c("Forest", "eastForest", "forest")){
modDat_1_s$uniqueID <- 1:nrow(modDat_1_s)
modDat_1_sf$uniqueID <- 1:nrow(modDat_1_sf)

# find which observations overlap with Louisiana
obs_LA_temp <- st_intersects(modDat_1_sf, cropped_states[cropped_states$NAME == "Louisiana",], sparse = FALSE)
if (sum(obs_LA_temp) > 0) {
 obs_LA_1 <- modDat_1_sf[which(obs_LA_temp == TRUE, arr.ind = TRUE)[,1],]
# now, find only those within the oversampled area (near the coast)
dims <- c(xmin = 730439.1, xmax = 1042195.5, ymax = -1222745.2, ymin = -1390430.9)
badBox <- st_bbox(dims) %>% 
  st_as_sfc() %>% 
  st_set_crs(value = st_crs(modDat_1_sf))
  
obs_LA_temp2 <- st_intersects(obs_LA_1, badBox, sparse = FALSE)
obs_LA_2 <- obs_LA_1[which(obs_LA_temp2 == TRUE, arr.ind = TRUE)[,1],]

# subsample so there aren't so many 
# get every 7th observation
obs_LA_sampled <- obs_LA_2[seq(from = 1, to = nrow(obs_LA_2), by = 10),]
# remove observations that aren't sampled from the larger dataset
obsToRemove <- obs_LA_2[!(obs_LA_2$uniqueID %in% obs_LA_sampled$uniqueID),]

modDat_1_sf <- modDat_1_sf[!(modDat_1_sf$uniqueID %in% obsToRemove$uniqueID),]
modDat_1_s <- modDat_1_s[!(modDat_1_s$uniqueID %in% obsToRemove$uniqueID),] 
}
}
## do a pca of climate across level 2 ecoregions
pca <- prcomp(modDat_1_s[,paste0(prednames)])
library(factoextra)
(fviz_pca_ind(pca, habillage = modDat_1_s$NA_L2NAME, label = "none", addEllipses = TRUE, ellipse.level = .95, ggtheme = theme_minimal(), alpha.ind = .1))

if (ecoregion == "shrubGrass") {
  print("We'll combine the 'Mediterranean California' and 'Western Sierra Madre Piedmont' ecoregions (into 'Mediterranean Piedmont'). We'll also combine `Tamaulipas-Texas semiarid plain,' 'Texas-Lousiana Coastal plain,' and 'South Central semiarid prairies' ecoregions (into (`Semiarid plain and prairies`)." )

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MEDITERRANEAN CALIFORNIA", "WESTERN SIERRA MADRE PIEDMONT"), "NA_L2NAME"] <- "MEDITERRANEAN PIEDMONT"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("TAMAULIPAS-TEXAS SEMIARID PLAIN", "TEXAS-LOUISIANA COASTAL PLAIN", "SOUTH CENTRAL SEMIARID PRAIRIES"), "NA_L2NAME"] <- "SEMIARID PLAIN AND PRAIRIES"

    modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MARINE WEST COAST FOREST", "WESTERN CORDILLERA"), "NA_L2NAME"] <- "WESTERN CORDILLERA AND WEST COAST FOREST"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MEDITERRANEAN CALIFORNIA", "UPPER GILA MOUNTAINS"), "NA_L2NAME"] <- "MEDITERRANEAN CALIFORNIA AND UPPER GILA MOUNTAINS"

modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MIXED WOOD PLAINS", "OZARK/OUACHITA-APPALACHIAN FORESTS"), "NA_L2NAME"] <- "OZARK/OUACHITA-APPALACHIAN FORESTS AND MIXED WOOD PLAINS"
#////
modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MEDITERRANEAN CALIFORNIA", "WESTERN SIERRA MADRE PIEDMONT"), "NA_L2NAME"] <- "MEDITERRANEAN PIEDMONT"

  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("TAMAULIPAS-TEXAS SEMIARID PLAIN", "TEXAS-LOUISIANA COASTAL PLAIN", "SOUTH CENTRAL SEMIARID PRAIRIES"), "NA_L2NAME"] <- "SEMIARID PLAIN AND PRAIRIES"

    modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MARINE WEST COAST FOREST", "WESTERN CORDILLERA"), "NA_L2NAME"] <- "WESTERN CORDILLERA AND WEST COAST FOREST"

  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MEDITERRANEAN CALIFORNIA", "UPPER GILA MOUNTAINS"), "NA_L2NAME"] <- "MEDITERRANEAN CALIFORNIA AND UPPER GILA MOUNTAINS"

modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MIXED WOOD PLAINS", "OZARK/OUACHITA-APPALACHIAN FORESTS"), "NA_L2NAME"] <- "OZARK/OUACHITA-APPALACHIAN FORESTS AND MIXED WOOD PLAINS"
 if (response == "CAMCover") {
   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MEDITERRANEAN PIEDMONT", "SEMIARID PLAIN AND PRAIRIES"), "NA_L2NAME"] <- "SEMIARID PLAIN AND PRAIRIES AND PIEDMONT"
   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MEDITERRANEAN PIEDMONT", "SEMIARID PLAIN AND PRAIRIES"), "NA_L2NAME"] <- "SEMIARID PLAIN AND PRAIRIES AND PIEDMONT"
 } else if (response %in% c("C4GramCover_prop", "C3GramCover_prop")) {
     modDat_1_s[modDat_1_s$NA_L2NAME %in% c("SEMIARID PLAIN AND PRAIRIES", "TEMPERATE PRAIRIES"), "NA_L2NAME"] <- "SEMIARID AND TEMPERATE PRAIRIES"
   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("SEMIARID PLAIN AND PRAIRIES", "TEMPERATE PRAIRIES"), "NA_L2NAME"] <- "SEMIARID AND TEMPERATE PRAIRIES"
 }

} else if (ecoregion == "CONUS") {

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("EVERGLADES", "MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"), "NA_L2NAME"] <- "EVERGLADES MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MARINE WEST COAST FOREST", "WESTERN CORDILLERA"), "NA_L2NAME"] <- "WESTERN CORDILLERA AND WEST COAST FOREST"

   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MIXED WOOD PLAINS", "OZARK/OUACHITA-APPALACHIAN FORESTS"), "NA_L2NAME"] <- "OZARK/OUACHITA-APPALACHIAN FORESTS AND MIXED WOOD PLAINS"

   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MEDITERRANEAN CALIFORNIA", "UPPER GILA MOUNTAINS"), "NA_L2NAME"] <- "MEDITERRANEAN CALIFORNIA AND UPPER GILA MOUNTAINS"

   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("OZARK/OUACHITA-APPALACHIAN FORESTS AND MIXED WOOD PLAINS", "SOUTHEASTERN USA PLAINS",  "MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS", "EVERGLADES MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN AND MIXED WOOD PLAINS"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("SOUTH CENTRAL SEMIARID PRAIRIES", "TEXAS-LOUISIANA COASTAL PLAIN"), "NA_L2NAME"] <- "SOUTH CENTRAL SEMIARID PRAIRIES"
  #///

  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("EVERGLADES", "MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"), "NA_L2NAME"] <- "EVERGLADES MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"

  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MARINE WEST COAST FOREST", "WESTERN CORDILLERA"), "NA_L2NAME"] <- "WESTERN CORDILLERA AND WEST COAST FOREST"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MIXED WOOD PLAINS", "OZARK/OUACHITA-APPALACHIAN FORESTS"), "NA_L2NAME"] <- "OZARK/OUACHITA-APPALACHIAN FORESTS AND MIXED WOOD PLAINS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MEDITERRANEAN CALIFORNIA", "UPPER GILA MOUNTAINS"), "NA_L2NAME"] <- "MEDITERRANEAN CALIFORNIA AND UPPER GILA MOUNTAINS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("OZARK/OUACHITA-APPALACHIAN FORESTS AND MIXED WOOD PLAINS", "SOUTHEASTERN USA PLAINS",  "MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS", "EVERGLADES MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN AND MIXED WOOD PLAINS"

  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("SOUTH CENTRAL SEMIARID PRAIRIES", "TEXAS-LOUISIANA COASTAL PLAIN"), "NA_L2NAME"] <- "SOUTH CENTRAL SEMIARID PRAIRIES"

  if (response %in% c("C4GramCover_prop")) {
    modDat_1_s[modDat_1_s$NA_L2NAME %in% c("CENTRAL USA PLAINS", "TEMPERATE PRAIRIES", "SOUTHEASTERN AND MIXED WOOD PLAINS", "ATLANTIC HIGHLANDS", "MIXED WOOD SHIELD"), "NA_L2NAME"] <- "EASTERN AND MIXED WOOD PLAINS AND FOREST"
  #///

  modDat_1_sf[modDat_1_sf$NA_L2NAME %in%c("CENTRAL USA PLAINS", "TEMPERATE PRAIRIES", "SOUTHEASTERN AND MIXED WOOD PLAINS", "ATLANTIC HIGHLANDS", "MIXED WOOD SHIELD"), "NA_L2NAME"] <- "EASTERN AND MIXED WOOD PLAINS AND FOREST"
  }
} else if (ecoregion == "forest"  & response != "CAMCover") {
   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS", "EVERGLADES"), "NA_L2NAME"] <- "MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS    AND EVERGLADES"

   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("UPPER GILA MOUNTAINS", "WESTERN CORDILLERA"), "NA_L2NAME"] <- "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS"

   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS\tAND EVERGLADES", "SOUTHEASTERN USA PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN USA PLAINS"

   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("ATLANTIC HIGHLANDS", "OZARK/OUACHITA-APPALACHIAN FORESTS"), "NA_L2NAME"] <- "HIGHLANDS AND APPALACHIAN FORESTS"

   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("CENTRAL USA PLAINS", "MIXED WOOD PLAINS"), "NA_L2NAME"] <- "CENTRAL AND MIXED WOOD PLAINS"

   modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MIXED WOOD SHIELD", "CENTRAL AND MIXED WOOD PLAINS"), "NA_L2NAME"] <- "CENTRAL AND MIXED WOOD PLAINS AND MIXED WOOD SHIELD"

       ## divide southeastern US plains into two regions, since it's by far the largest group
  modDat_1_s[modDat_1_s$NA_L2NAME == "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS" &
               modDat_1_s$Long < -966595#-1773969
               , "NA_L2NAME"] <- "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 1"
  modDat_1_s[modDat_1_s$NA_L2NAME == "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS", "NA_L2NAME"] <- "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 2"
   #///
   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS", "EVERGLADES"), "NA_L2NAME"] <- "MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS  AND EVERGLADES"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("UPPER GILA MOUNTAINS", "WESTERN CORDILLERA"), "NA_L2NAME"] <- "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS\tAND EVERGLADES", "SOUTHEASTERN USA PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN USA PLAINS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("ATLANTIC HIGHLANDS", "OZARK/OUACHITA-APPALACHIAN FORESTS"), "NA_L2NAME"] <- "HIGHLANDS AND APPALACHIAN FORESTS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("CENTRAL USA PLAINS", "MIXED WOOD PLAINS"), "NA_L2NAME"] <- "CENTRAL AND MIXED WOOD PLAINS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MIXED WOOD SHIELD", "CENTRAL AND MIXED WOOD PLAINS"), "NA_L2NAME"] <- "CENTRAL AND MIXED WOOD PLAINS AND MIXED WOOD SHIELD"
          ## divide southeastern US plains into two regions, since it's by far the largest group
  modDat_1_sf[modDat_1_sf$NA_L2NAME == "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS" &
              st_coordinates(modDat_1_sf)[,1] < -966595#-1773969
                , ]$NA_L2NAME <- "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 1"
  modDat_1_sf[modDat_1_sf$NA_L2NAME == "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS", "NA_L2NAME"] <- "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 2"

  if (response %in% c("C3GramCover_prop", "C4GramCover_prop") ) {
     modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MARINE WEST COAST FOREST", "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 1"), "NA_L2NAME"] <- "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 1"
     modDat_1_s[modDat_1_s$NA_L2NAME %in% c("CENTRAL AND MIXED WOOD PLAINS AND MIXED WOOD SHIELD", "HIGHLANDS AND APPALACHIAN FORESTS"), "NA_L2NAME"] <- "CENTRAL AND MIXED WOODS AND HIGHLANDS FORESTS"
     #//
  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MARINE WEST COAST FOREST", "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 1"), "NA_L2NAME"] <- "WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 1"
  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("CENTRAL AND MIXED WOOD PLAINS AND MIXED WOOD SHIELD", "HIGHLANDS AND APPALACHIAN FORESTS"), "NA_L2NAME"] <- "CENTRAL AND MIXED WOODS AND HIGHLANDS FORESTS"

  }

} else if (ecoregion == "forest" & response == "CAMCover") {

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("OZARK/OUACHITA-APPALACHIAN FORESTS", "SOUTHEASTERN USA PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN PLAINS AND APPALACHIAN FORESTS"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MARINE WEST COAST FOREST", "WESTERN CORDILLERA"), "NA_L2NAME"] <- "MARINE WEST COAST AND WESTERN CORDILLERA"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MIXED WOOD PLAINS", "SOUTHEASTERN PLAINS AND APPALACHIAN FORESTS"), "NA_L2NAME"] <- "SOUTHEASTERN PLAINS AND APPALACHIAN FORESTS"

  #///
   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("OZARK/OUACHITA-APPALACHIAN FORESTS", "SOUTHEASTERN USA PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN PLAINS AND APPALACHIAN FORESTS"

  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MARINE WEST COAST FOREST", "WESTERN CORDILLERA"), "NA_L2NAME"] <- "MARINE WEST COAST AND WESTERN CORDILLERA"

  modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MIXED WOOD PLAINS", "SOUTHEASTERN PLAINS AND APPALACHIAN FORESTS"), "NA_L2NAME"] <- "SOUTHEASTERN PLAINS AND APPALACHIAN FORESTS"

} else if (ecoregion == "eastForest") {
  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("EVERGLADES", "MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"), "NA_L2NAME"] <- "EVERGLADES MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MIXED WOOD PLAINS","CENTRAL USA PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN AND CENTRAL USA PLAINS"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MIXED WOOD SHIELD", "ATLANTIC HIGHLANDS"), "NA_L2NAME"] <- "ATLANTIC HIGHLANDS AND MIXED WOOD SHIELD"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("MIXED WOOD PLAINS", "ATLANTIC HIGHLANDS AND MIXED WOOD SHIELD"), "NA_L2NAME"] <- "ATLANTIC HIGHLANDS AND MIXED WOOD SHIELD AND PLAINS"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("SOUTHEASTERN AND CENTRAL USA PLAINS", "ATLANTIC HIGHLANDS AND MIXED WOOD SHIELD AND PLAINS"), "NA_L2NAME"] <- "PLAINS AND HIGHLANDS AND SHIELD"

  modDat_1_s[modDat_1_s$NA_L2NAME %in% c("EVERGLADES MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS", "SOUTHEASTERN USA PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN PLAINS AND COAST"

  # #////
   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("EVERGLADES", "MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"), "NA_L2NAME"] <- "EVERGLADES MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MIXED WOOD PLAINS","CENTRAL USA PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN AND CENTRAL USA PLAINS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MIXED WOOD SHIELD", "ATLANTIC HIGHLANDS"), "NA_L2NAME"] <- "ATLANTIC HIGHLANDS AND MIXED WOOD SHIELD"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("MIXED WOOD PLAINS", "ATLANTIC HIGHLANDS AND MIXED WOOD SHIELD"), "NA_L2NAME"] <- "ATLANTIC HIGHLANDS AND MIXED WOOD SHIELD AND PLAINS"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("SOUTHEASTERN AND CENTRAL USA PLAINS", "ATLANTIC HIGHLANDS AND MIXED WOOD SHIELD AND PLAINS"), "NA_L2NAME"] <- "PLAINS AND HIGHLANDS AND SHIELD"

   modDat_1_sf[modDat_1_sf$NA_L2NAME %in% c("EVERGLADES MISSISSIPPI ALLUVIAL AND SOUTHEAST USA COASTAL PLAINS", "SOUTHEASTERN USA PLAINS"), "NA_L2NAME"] <- "SOUTHEASTERN PLAINS AND COAST"

   ## divide southeastern US plains into two regions, since it's by far the largest group
  # modDat_1_s[modDat_1_s$NA_L2NAME == "SOUTHEASTERN USA PLAINS" &
  #              modDat_1_s$Lat < -590062, "NA_L2NAME"] <- "SOUTHEASTERN USA PLAINS 1"
  # modDat_1_s[modDat_1_s$NA_L2NAME == "SOUTHEASTERN USA PLAINS", #&
  #             # modDat_1_s$Lat < -590062,
  #            "NA_L2NAME"] <- "SOUTHEASTERN USA PLAINS 2"

  #   ## divide southeastern US plains into two regions, since it's by far the largest group
  # modDat_1_s[modDat_1_s$NA_L2NAME == "OZARK/OUACHITA-APPALACHIAN FORESTS" &
  #              modDat_1_s$Long < 854862.2, "NA_L2NAME"] <- "OZARK/OUACHITA-APPALACHIAN FORESTS 1"
  # modDat_1_s[modDat_1_s$NA_L2NAME == "OZARK/OUACHITA-APPALACHIAN FORESTS" &
  #              modDat_1_s$Long  >=   854862.2, "NA_L2NAME"] <- "OZARK/OUACHITA-APPALACHIAN FORESTS 2"
}
# make a table of n for each region
modDat_1_s %>% 
  group_by(NA_L2NAME) %>% 
  dplyr::summarize("Number_Of_Observations" = length(NA_L2NAME)) %>% 
  rename("Level_2_Ecoregion" = NA_L2NAME)%>% 
  kable() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed")) 
Level_2_Ecoregion Number_Of_Observations
CENTRAL AND MIXED WOOD PLAINS AND MIXED WOOD SHIELD 3662
HIGHLANDS AND APPALACHIAN FORESTS 3845
MARINE WEST COAST FOREST 5485
SOUTHEASTERN USA PLAINS 4907
WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 1 34496
WESTERN CORDILLERA AND UPPER GILA MOUNTAINS 2 20538

Then, look at the spatial distribution and environmental characteristics of the grouped ecoregions

map1 <- ggplot() +
  geom_sf(data=cropped_states,fill='white') +
  geom_sf(data=modDat_1_sf#[modDat_1_sf$NA_L2NAME %in% c("MIXED WOOD PLAINS"),]
          ,
          aes(fill=as.factor(NA_L2NAME)),linewidth=0.5,alpha=0.5) +
  geom_point(data=modDat_1_s#[modDat_1_s$NA_L2NAME %in% c("MIXED WOOD PLAINS"),]
             ,
             alpha=0.5, 
             aes(x = Long, y = Lat, color=as.factor(NA_L2NAME)), alpha = .1) +
  #scale_fill_okabeito() +
  #scale_color_okabeito() +
 # theme_default() +
  theme(legend.position = 'none') +
  labs(title = "Level 2 Ecoregions as spatial blocks")

hull <- modDat_1_sf %>%
  ungroup() %>%
  group_by(NA_L2NAME) %>%
  slice(chull(tmean, prcp))

plot1<-ggplot(data=modDat_1_sf,aes(x=tmean,y=prcp)) +
  geom_polygon(data = hull, alpha = 0.25,aes(fill=NA_L2NAME) )+
  geom_point(aes(group=NA_L2NAME,color=NA_L2NAME),alpha=0.25) +
  theme_minimal() + xlab("Annual Average T_mean - long-term average") +
  ylab("Annual Average Precip - long-term average") #+
  #scale_color_okabeito() +
  #scale_fill_okabeito()

plot2<-ggplot(data=modDat_1_sf %>%
                pivot_longer(cols=tmean:prcp),
              aes(x=value,group=name)) +
  # geom_polygon(data = hull, alpha = 0.25,aes(fill=fold) )+
  geom_density(aes(group=NA_L2NAME,fill=NA_L2NAME),alpha=0.25) +
  theme_minimal() +
  facet_wrap(~name,scales='free')# +
  #scale_color_okabeito() +
  #scale_fill_okabeito()
 
library(patchwork)
(combo <- (map1+plot1)/plot2) 

# 
# ggplot(data = modDat_1_s) +
#   geom_density(aes(ShrubCover_transformed, col = NA_L2NAME)) +
#   xlim(c(0,100))

Fit a global model with all of the data

First, fit a LASSO regression model using the glmnet R package

  • This regression is a beta glm with a logit link (using custom function from Daniel)
  • Use cross validation across level 2 ecoregions to tune the lambda parameter in the LASSO model
  • this model is fit to using the scaled weather/climate/soils variables
  • this list of possible predictors includes:
    1. main effects
    2. interactions between all soils variables
    3. interactions between climate and weather variables
    4. transformed main effects (squared, log-transformed (add a uniform integer – 20– to all variables prior to log-transformation), square root-transformed (add a uniform integer – 20– to all variables prior to log-transformation))

Get rid of transformed predictions and interactions that are correlated

# get first pass of names correlated variables
X_df <- X %>% 
  as.data.frame() %>% 
  dplyr::select(-'(Intercept)')  
corrNames_i <- X_df %>% 
  cor()  %>% 
   caret::findCorrelation(cutoff = .7, verbose = FALSE, names = TRUE, exact = TRUE)
# remove those names that are untransformed main effects 
  # vector of columns to remove 
badNames <- corrNames_i[!(corrNames_i %in% prednames)]
while (sum(!(corrNames_i %in% prednames))>0) {
 corrNames_i <-  X_df %>% 
    dplyr::select(-badNames) %>% 
     cor()  %>% 
   caret::findCorrelation(cutoff = .7, verbose = FALSE, names = TRUE, exact = TRUE)
 # update the vector of names to remove 
 badNames <- unique(c(badNames, corrNames_i[!(corrNames_i %in% prednames)]))
}

## see if there are any correlated variables left (would be all main effects at this point)
# if there are, step through and remove the variable that each is most correlated with 
if (length(corrNames_i)>1) {
  for (i in 1:length(corrNames_i)) {
    X_i <- X_df %>% 
      dplyr::select(-badNames)
    if (corrNames_i[i] %in% names(X_i)) {
    corMat_i <- cor(x = X_i[corrNames_i[i]], y = X_i %>% dplyr::select(-corrNames_i[i])) 
    badNames_i <- colnames(corMat_i)[abs(corMat_i)>=.7]
    # if there are any predictors in the 'badNames_i', remove them from this list
    if (length(badNames_i) > 0 & sum(c(badNames_i %in% prednames))>0) {
        badNames_i <- badNames_i[!(badNames_i %in% prednames)]
    }
    badNames <- unique(c(badNames, badNames_i))
    }
  }
}
## update the X matrix to exclude these correlated variables
X <- X[,!(colnames(X) %in% badNames)]
if (run == TRUE) {
  # set up custom folds
    # get the ecoregions for training lambda
  train_eco <- modDat_1_s$NA_L2NAME#[train]
  
  # Fit model -----------------------------------------------
  # specify leave-one-year-out cross-validation
  my_folds <- as.numeric(as.factor(train_eco))

    # set up parallel processing
    library(doMC)
    # this computer has 16 cores (parallel::detectCores())
    registerDoMC(cores = 8)
    
    fit <- cv.glmnet(
      x = X[,2:ncol(X)], 
      y = y, 
      family = quasibeta_family(),
      keep = FALSE,
      alpha = 1,  # 0 == ridge regression, 1 == lasso, 0.5 ~~ elastic net
      lambda = lambdas,
      relax = ifelse(response == "ShrubCover", yes = TRUE, no = FALSE),
      #nlambda = 100,
      type.measure="mse",
      #penalty.factor = pen_facts,
      foldid = my_folds,
      #thresh = thresh,
      standardize = FALSE, ## scales variables prior to the model sequence... coefficients are always returned on the original scale
      parallel = TRUE
    )
    base::saveRDS(fit, paste0("../ModelFitting/models/betaLASSO/", response, "_globalLASSOmod_betaLogitLink_",ecoregion,".rds"))
    
  } else {
    fit <- readRDS(paste0("../ModelFitting/models/betaLASSO/", response, "_globalLASSOmod_betaLogitLink_",ecoregion,".rds"))
  }


  # assess model fit
  # assess.glmnet(fit$fit.preval, #newx = X[,2:293], 
  #               newy = y, family = stats::Gamma(link = "log"))
  # save the minimum lambda
  best_lambda <- fit$lambda.min
  # save the lambda for the most regularized model w/ an MSE that is still 1SE w/in the best lambda model
  lambda_1SE <- fit$lambda.1se
  # save the lambda for the most regularized model w/ an MSE that is still .5SE w/in the best lambda model
  lambda_halfSE <- best_lambda + ((lambda_1SE - best_lambda)/2)
 
  print(fit)     
## 
## Call:  cv.glmnet(x = X[, 2:ncol(X)], y = y, lambda = lambdas, type.measure = "mse",      foldid = my_folds, keep = FALSE, parallel = TRUE, relax = ifelse(response ==          "ShrubCover", yes = TRUE, no = FALSE), family = quasibeta_family(),      alpha = 1, standardize = FALSE) 
## 
## Measure: Mean-Squared Error 
## 
##       Lambda Index Measure       SE Nonzero
## min 0.001956   124 0.06103 0.007825      94
## 1se 0.027364    86 0.06839 0.009465      19
  plot(fit)

Now, we need to do stability selection to ensure the coefficients that are being chosen with each lambda are stable

## stability selection for best lambda model 
# setup params
p <- ncol(X[,2:ncol(X)]) # of parameters
n <- length(y) # of observations
n_iter <- 100        # number of subsamples
sample_frac <- 0.75  # fraction of data to subsample
lambda_val <- best_lambda    # fixed lambda value (could be chosen via CV)

# Track selection
selection_counts <- matrix(0, nrow = p, ncol = 1)

for (i in 1:n_iter) {
  # Subsample rows
  sample_idx <- sample(1:n, size = floor(sample_frac * n), replace = FALSE)
  X_sub <- X[sample_idx, ]
  y_sub <- y[sample_idx]

  # Fit Lasso model
  fit_stab_i <- glmnet(x = X_sub[,2:ncol(X_sub)], y = y_sub, 
    family = quasibeta_family(),
    alpha = 1, lambda = lambda_val, standardize = FALSE)

  # Get non-zero coefficients (excluding intercept)
  selected <- which(as.vector(coef(fit_stab_i))[-1] != 0)
  selection_counts[selected] <- selection_counts[selected] + 1
}

# Convert counts to selection probabilities (the probability that a variable is selected over 100 iterations)
selection_prob <- selection_counts / n_iter
selection_prob_df <- data.frame(
  VariableNumber = paste0("X", 1:p),
  VariableName = rownames(coef(fit_stab_i))[2:(p+1)],
  SelectionProb = as.vector(selection_prob)
)

# get those variables that are selected in ≥70% of subsets (Meinshausen and Bühlmann, 2010)
bestLambda_coef <- selection_prob_df[selection_prob_df$SelectionProb>=.7, c("VariableName", "SelectionProb")]

#//////
# stability selection for 1se lambda model
lambda_val <-  lambda_1SE    # fixed lambda value (could be chosen via CV)

# Track selection
selection_counts <- matrix(0, nrow = p, ncol = 1)

for (i in 1:n_iter) {
  # Subsample rows
  sample_idx <- sample(1:n, size = floor(sample_frac * n), replace = FALSE)
  X_sub <- X[sample_idx, ]
  y_sub <- y[sample_idx]

  # Fit Lasso model
  fit_stab_i <- glmnet(x = X_sub[,2:ncol(X_sub)], y = y_sub, 
    family = quasibeta_family(),
    alpha = 1, lambda = lambda_val, standardize = FALSE)

  # Get non-zero coefficients (excluding intercept)
  selected <- which(as.vector(coef(fit_stab_i))[-1] != 0)
  selection_counts[selected] <- selection_counts[selected] + 1
}

# Convert counts to selection probabilities (the probability that a variable is selected over 100 iterations)
selection_prob <- selection_counts / n_iter
selection_prob_df <- data.frame(
  VariableNumber = paste0("X", 1:p),
  VariableName = rownames(coef(fit_stab_i))[2:(p+1)],
  SelectionProb = as.vector(selection_prob)
)

# get those variables that are selected in ≥70% of subsets (Meinshausen and Bühlmann, 2010)
seLambda_coef <- selection_prob_df[selection_prob_df$SelectionProb>=.7, c("VariableName", "SelectionProb")]

#//////
# stability selection for half se lambda model
lambda_val <- lambda_halfSE    # fixed lambda value (could be chosen via CV)

# Track selection
selection_counts <- matrix(0, nrow = p, ncol = 1)

for (i in 1:n_iter) {
  # Subsample rows
  sample_idx <- sample(1:n, size = floor(sample_frac * n), replace = FALSE)
  X_sub <- X[sample_idx, ]
  y_sub <- y[sample_idx]

  # Fit Lasso model
  fit_stab_i <- glmnet(x = X_sub[,2:ncol(X_sub)], y = y_sub, 
    family = stats::Gamma(link = "log"),
    alpha = 1, lambda = lambda_val, standardize = FALSE)

  # Get non-zero coefficients (excluding intercept)
  selected <- which(as.vector(coef(fit_stab_i))[-1] != 0)
  selection_counts[selected] <- selection_counts[selected] + 1
}

# Convert counts to selection probabilities (the probability that a variable is selected over 100 iterations)
selection_prob <- selection_counts / n_iter
selection_prob_df <- data.frame(
  VariableNumber = paste0("X", 1:p),
  VariableName = rownames(coef(fit_stab_i))[2:(p+1)],
  SelectionProb = as.vector(selection_prob)
)

# get those variables that are selected in ≥70% of subsets (Meinshausen and Bühlmann, 2010)
halfseLambda_coef <- selection_prob_df[selection_prob_df$SelectionProb>=.7, c("VariableName", "SelectionProb")]

If prompted to do so by the input arguments, remove any predictors that are for weather anomalies whose corresponding climate predictor is not included in the model

if (trimAnom == TRUE) {
  # get unique predictors
  bestLamb_all <- bestLambda_coef$VariableName %>% #[str_detect(bestLambda_coef$VariableName, pattern = "_anom_s")] %>% 
    str_remove(pattern = "I\\(") %>% 
    str_remove(pattern = "\\^2\\)") %>% 
    str_remove(pattern = "\\^2\\)") %>% 
    str_split(pattern = ":", simplify = TRUE) 
  if (ncol(bestLamb_all) == 1) {
    bestLamb_all <- unique(bestLamb_all)
  } else {
    bestLamb_all <-  c(bestLamb_all[bestLamb_all[,1] !="",1], bestLamb_all[bestLamb_all[,2] !="",2]) %>% 
      unique()
  }
  # get anomalies
   bestLamb_anom <- bestLamb_all[bestLamb_all %in% prednames_weath]
  # get climate
   bestLamb_clim <- bestLamb_all[bestLamb_all %in% prednames_clim]
  # which anomalies are present in the predictors, but their corresponding climate variable isn't
   bestLamb_anomsWithMissingClim <- bestLamb_anom[!(str_remove(bestLamb_anom, "_anom") %in% bestLamb_clim)]
   # remove anomalies (and all interaction terms w/ those anomalies) from the predictor list

   if (length(bestLamb_anomsWithMissingClim) != 0) {
   
        bestLambda_coef_NEW <- bestLambda_coef
      for (i in 1:length(bestLamb_anomsWithMissingClim)) {
     bestLambda_coef_NEW <- bestLambda_coef_NEW[!str_detect(bestLambda_coef_NEW$VariableName, pattern = bestLamb_anomsWithMissingClim[i]),]
      }
     
   bestLambda_coef <- bestLambda_coef_NEW
   }
   
   
  #//// 1 se lambda model
      if (nrow(seLambda_coef) !=0) {
        # get unique predictors
  seLamb_all <- seLambda_coef$VariableName %>% #[str_detect(seLambda_coef$VariableName, pattern = "_anom_s")] %>% 
    str_remove(pattern = "I\\(") %>% 
    str_remove(pattern = "_s\\^2\\)") %>% 
    str_remove(pattern = "\\^2\\)") %>% 
    str_split(pattern = ":", simplify = TRUE) 
  if (ncol(seLamb_all) == 1) {
    seLamb_all <- unique(seLamb_all)
  } else {
    seLamb_all <-  c(seLamb_all[seLamb_all[,1] !="",1], seLamb_all[seLamb_all[,2] !="",2]) %>% 
      unique()
  }
  # get anomalies
   seLamb_anom <- seLamb_all[seLamb_all %in% prednames_weath]
  # get climate
   seLamb_clim <- seLamb_all[seLamb_all %in% prednames_clim]
  # which anomalies are present in the predictors, but their corresponding climate variable isn't
   seLamb_anomsWithMissingClim <- seLamb_anom[!(str_remove(seLamb_anom, "_anom") %in%  seLamb_clim)]
   # remove anomalies (and all interaction terms w/ those anomalies) from the predictor list
      if (length(seLamb_anomsWithMissingClim) != 0) {
    seLambda_coef_NEW <- seLambda_coef
   for (i in 1:length(seLamb_anomsWithMissingClim)) {
     seLambda_coef_NEW <- seLambda_coef_NEW[!str_detect(seLambda_coef_NEW$VariableName, pattern = seLamb_anomsWithMissingClim[i]),]
   }
   seLambda_coef <- seLambda_coef_NEW
      }
   }
  
  #//// 1 se lambda model
      if (nrow(halfseLambda_coef) !=0) {
        # get unique predictors
  halfseLamball<- halfseLambda_coef$VariableName %>% #[str_detect(halfseLambda_coef$VariableName, pattern = "_anom_s")] %>% 
    str_remove(pattern = "I\\(") %>% 
    str_remove(pattern = "_s\\^2\\)") %>% 
    str_split(pattern = ":", simplify = TRUE) 
  
    if (ncol(halfseLamball) == 1) {
    halfseLamball <- unique(halfseLamball)
  } else {
    halfseLamball <-  c(halfseLamball[halfseLamball[,1] !="",1], halfseLamball[halfseLamball[,2] !="",2]) %>% 
      unique()
  }
  
  # get anomalies
   halfseLambanom <- halfseLamball[halfseLamball %in% prednames_weath]
  # get climate
   halfseLambclim <- halfseLamball[halfseLamball %in% prednames_clim]
  # which anomalies are present in the predictors, but their corresponding climate variable isn't
   halfseLambanomsWithMissingClim <- halfseLambanom[!(str_remove(halfseLambanom, "_anom_s") %in%  halfseLambclim)]
   # remove anomalies (and all interaction terms w/ those anomalies) from the predictor list

   
   ##
        if (length(halfseLambanomsWithMissingClim) != 0) {
   halfseLambda_coef_NEW <- halfseLambda_coef
   for (i in 1:length(halfseLambanomsWithMissingClim)) {
     halfseLambda_coef_NEW <- halfseLambda_coef_NEW[!str_detect(halfseLambda_coef_NEW$VariableName, pattern = halfseLambanomsWithMissingClim[i]),]
   }
   halfseLambda_coef <- halfseLambda_coef_NEW
      }
   }
    ##
  
      }

Then, fit regular glm models (Beta glm with a logit link), first using the coefficients from the ‘best’ lambda identified in the LASSO model, and then using the coefficients from the ‘1SE’ lambda and then the ‘1/2SE’ lambda values identified from the LASSO (this is the value of lambda such that the cross validation error is within 1 standard error of the minimum).

## fit w/ the identified coefficients from the 'best' lambda, but using the glm function
  mat_glmnet_best <- bestLambda_coef$VariableName 

  if (length(mat_glmnet_best) == 0) {
    f_glm_bestLambda <- as.formula(paste0(response_t, "~ 1"))
  } else {
  f_glm_bestLambda <- as.formula(paste0(response_t, " ~ ", paste0(mat_glmnet_best, collapse = " + ")))
  }
  
## fit using betareg
  fit_glm_bestLambda <- fit_glm_bestLambda_quasiBETA <- glm(formula = f_glm_bestLambda, data = modDat_1_s, family =quasibeta_family(link = "logit") )
    
  #fit_glm_bestLambda_BETAREG <- betareg(formula =  f_glm_bestLambda, data = modDat_1_s, link = "logit")
  ## fit using quasi-beta
  # ## compare coefficients
  # modCoeffsTest <- data.frame("coefficientName" = names(coefficients(fit_glm_bestLambda_BETAREG)),
  #                             "coefficientValue" = coefficients(fit_glm_bestLambda_BETAREG), 
  #                             "confint_low" = confint(fit_glm_bestLambda_BETAREG)[,1],
  #                             "confint_high" = confint(fit_glm_bestLambda_BETAREG)[,2],
  #                             "type" = "betareg") %>% 
  #   rbind(data.frame("coefficientName" = names(coefficients(fit_glm_bestLambda_quasiBETA)),
  #                             "coefficientValue" = coefficients(fit_glm_bestLambda_quasiBETA), 
  #                             "confint_low" = coefficients(fit_glm_bestLambda_quasiBETA) - ( summary(fit_glm_bestLambda_quasiBETA)$coefficients[,2] * 1.96) ,
  #                             "confint_high" = coefficients(fit_glm_bestLambda_quasiBETA) + ( summary(fit_glm_bestLambda_quasiBETA)$coefficients[,2] * 1.96),
  #                             "type" = "quasiBeta")) %>% 
  #   filter(coefficientName != "(phi)")
  # ggplot(data = modCoeffsTest) + 
  #   geom_point(aes(x = coefficientValue, y = coefficientName, col = type)) + 
  #   geom_errorbar(aes(xmin = confint_low, xmax = confint_high, y = coefficientName, col = type)) + 
  #   geom_vline(aes(xintercept = 0), lty = 3)
  # 
   ## fit w/ the identified coefficients from the '1se' lambda, but using the glm function
  mat_glmnet_1se <- seLambda_coef$VariableName
    
  if (length(mat_glmnet_1se) == 0) {
    f_glm_1se <- as.formula(paste0(response_t, "~ 1"))
  } else {
  f_glm_1se <- as.formula(paste0(response_t, " ~ ", paste0(mat_glmnet_1se, collapse = " + ")))
  }


  fit_glm_se <- glm(formula = f_glm_1se, data = modDat_1_s, family =quasibeta_family(link = "logit") )
  # glm(data = modDat_1_s, formula = f_glm_1se,
  #                   family =  stats::Gamma(link = "log"))
  
     ## fit w/ the identified coefficients from the '.5se' lambda, but using the glm function
  mat_glmnet_halfse <- halfseLambda_coef$VariableName
  
  if (length(mat_glmnet_halfse) == 0) {
    f_glm_halfse <- as.formula(paste0(response_t, "~ 1"))
  } else {
  f_glm_halfse <- as.formula(paste0(response_t, " ~ ", paste0(mat_glmnet_halfse, collapse = " + ")))
  }

  fit_glm_halfse <- glm(formula = f_glm_halfse, data = modDat_1_s, family =quasibeta_family(link = "logit") )
  
  #glm(data = modDat_1_s, formula =  f_glm_halfse,
                   # family =  stats::Gamma(link = "log"))
  
  ## save models 
  if (trimAnom == TRUE) {
    saveRDS(fit_glm_bestLambda, paste0("/Users/astears/Documents/Dropbox_static/Work/NAU_USGS_postdoc/PED_vegClimModels/Analysis/VegComposition/ModelFitting/models/",response,"_",ecoregion, "_noTLP_",removeTLP,"_trimAnom_bestLambdaGLM.rds"))
  saveRDS(fit_glm_halfse, paste0("/Users/astears/Documents/Dropbox_static/Work/NAU_USGS_postdoc/PED_vegClimModels/Analysis/VegComposition/ModelFitting/models/",response,"_",ecoregion, "_noTLP_",removeTLP,"_trimAnom_halfSELambdaGLM.rds"))
  saveRDS(fit_glm_se, paste0("/Users/astears/Documents/Dropbox_static/Work/NAU_USGS_postdoc/PED_vegClimModels/Analysis/VegComposition/ModelFitting/models/",response,"_",ecoregion, "_noTLP_",removeTLP,"_trimAnom_oneSELambdaGLM.rds"))
  } else {
    saveRDS(fit_glm_bestLambda, paste0("/Users/astears/Documents/Dropbox_static/Work/NAU_USGS_postdoc/PED_vegClimModels/Analysis/VegComposition/ModelFitting/models/",response,"_",ecoregion, "_noTLP_",removeTLP,"_bestLambdaGLM.rds"))
  saveRDS(fit_glm_halfse, paste0("/Users/astears/Documents/Dropbox_static/Work/NAU_USGS_postdoc/PED_vegClimModels/Analysis/VegComposition/ModelFitting/models/",response,"_",ecoregion, "_noTLP_",removeTLP,"_halfSELambdaGLM.rds"))
  saveRDS(fit_glm_se, paste0("/Users/astears/Documents/Dropbox_static/Work/NAU_USGS_postdoc/PED_vegClimModels/Analysis/VegComposition/ModelFitting/models/",response,"_",ecoregion, "_noTLP_",removeTLP,"_oneSELambdaGLM.rds"))
    
  }

Then, we predict (on the training set) using both of these models (best lambda and 1se lambda)

  ## predict on the test data
  # lasso model predictions with the optimal lambda
  optimal_pred <- predict(fit_glm_bestLambda, newx=X[,2:ncol(X)], type = "response")
  optimal_pred_1se <-  predict(fit_glm_se, newx=X[,2:ncol(X)], type = "response")
  optimal_pred_halfse <- predict(fit_glm_halfse, newx = X[,2:ncol(X)], type = "response")
  
    null_fit <- glm(#data = data.frame("y" = y, X[,paste0(prednames, "_s")]), 
      formula = y ~ 1, family = stats::Gamma(link = "log"))
  null_pred <- predict(null_fit, newdata = as.data.frame(X), type = "response"
                       )

  ## snap values above 100 and below 0 to be 100 or z
  #optimal_pred[optimal_pred>100] <- 100
  optimal_pred[optimal_pred<0] <- 0
  #optimal_pred_1se[optimal_pred_1se>100] <- 100
  optimal_pred_1se[optimal_pred_1se<0] <- 0
  #optimal_pred_halfse[optimal_pred_halfse>100] <- 100
  optimal_pred_halfse[optimal_pred_halfse<0] <- 0
  
  # save data
  fullModOut <- list(
    "modelObject" = fit,
    "nullModelObject" = null_fit,
    "modelPredictions" = data.frame(#ecoRegion_holdout = rep(test_eco,length(y)),
      obs=y,
                    pred_opt=optimal_pred, 
                    pred_opt_se = optimal_pred_1se,
                    pred_opt_halfse = optimal_pred_halfse,
                    pred_null=null_pred#,
                    #pred_nopenalty=nopen_pred
                    ))
  
# # calculate correlations between null and optimal model 
# my_cors <- c(cor(optimal_pred, c(y)),
#              cor(optimal_pred_1se, c(y)), 
#             cor(null_pred, c(y))
#             )
# 
# # calculate mse between null and optimal model 
# my_mse <- c(mean((fullModOut$modelPredictions$pred_opt -  c(y))^2) ,
#             mean((fullModOut$modelPredictions$pred_opt_se -  c(y))^2) ,
#             mean((fullModOut$modelPredictions$pred_null - c(y))^2)#,
#             #mean((obs_pred$pred_nopenalty - obs_pred$obs)^2)
#             )

ggplot() + 
  geom_point(aes(X[,2], fullModOut$modelPredictions$obs), col = "black", alpha = .1) + 
  geom_point(aes(X[,2], fullModOut$modelPredictions$pred_opt), col = "red", alpha = .1) + ## predictions w/ the CV model
  geom_point(aes(X[,2], fullModOut$modelPredictions$pred_opt_halfse), col = "orange", alpha = .1) + ## predictions w/ the CV model (.5se lambda)
  geom_point(aes(X[,2], fullModOut$modelPredictions$pred_opt_se), col = "green", alpha = .1) + ## predictions w/ the CV model (1se lambda)
  geom_point(aes(X[,2], fullModOut$modelPredictions$pred_null), col = "blue", alpha = .1) + 
  labs(title = "A rough comparison of observed and model-predicted values", 
       subtitle = "black = observed values \n red = predictions from 'best lambda' model \n orange = predictions for '1/2se' lambda model \n green = predictions from '1se' lambda model \n blue = predictions from null model") +
  xlab(colnames(X)[2])

  #ylim(c(0,200))

The internal cross-validation process to fit the global LASSO model identified an optimal lambda value (regularization parameter) of r{print(best_lambda)}. The lambda value such that the cross validation error is within 1 standard error of the minimum (“1se lambda”) was `r{print(fit$lambda.1se)}`` . The following coefficients were kept in each model:

# the coefficient matrix from the 'best model' -- find and print those coefficients that aren't 0 in a table
coef_glm_bestLambda <- coef(fit_glm_bestLambda) %>% 
  data.frame() 
coef_glm_bestLambda$coefficientName <- rownames(coef_glm_bestLambda)
names(coef_glm_bestLambda)[1] <- "coefficientValue_bestLambda"
# coefficient matrix from the '1se' model 
coef_glm_1se <- coef(fit_glm_se) %>% 
  data.frame() 
coef_glm_1se$coefficientName <- rownames(coef_glm_1se)
names(coef_glm_1se)[1] <- "coefficientValue_1seLambda"
# coefficient matrix from the 'half se' model 
coef_glm_halfse <- coef(fit_glm_halfse) %>% 
  data.frame() 
coef_glm_halfse$coefficientName <- rownames(coef_glm_halfse)
names(coef_glm_halfse)[1] <- "coefficientValue_halfseLambda"
# add together
coefs <- full_join(coef_glm_bestLambda, coef_glm_halfse) %>% 
  full_join(coef_glm_1se) %>% 
  dplyr::select(coefficientName, coefficientValue_bestLambda,
                coefficientValue_halfseLambda, coefficientValue_1seLambda)

globModTerms <- coefs[!is.na(coefs$coefficientValue_bestLambda), "coefficientName"]

## also, get the number of unique variables in each model 
var_prop_pred <- paste0(response, "_pred")
response_vars <- c(response, var_prop_pred)
# for best lambda model
prednames_fig <- paste(str_split(globModTerms, ":", simplify = TRUE)) 
prednames_fig <- str_replace(prednames_fig, "I\\(", "")
prednames_fig <- str_replace(prednames_fig, "\\^2\\)", "")
prednames_fig <- unique(prednames_fig[prednames_fig>0])
prednames_fig <- prednames_fig
prednames_fig_num <- length(prednames_fig)
# for 1SE lambda model
globModTerms_1se <- coefs[!is.na(coefs$coefficientValue_1seLambda), "coefficientName"]
if (length(globModTerms_1se) == 1) {
prednames_fig_1se <- paste(str_split(globModTerms_1se, ":", simplify = TRUE)) 
prednames_fig_1se <- str_replace(prednames_fig_1se, "I\\(", "")
prednames_fig_1se <- str_replace(prednames_fig_1se, "\\^2\\)", "")
prednames_fig_1se <- unique(prednames_fig_1se[prednames_fig_1se>0])
prednames_fig_1se_num <- c(0)
} else {
prednames_fig_1se <- paste(str_split(globModTerms_1se, ":", simplify = TRUE)) 
prednames_fig_1se <- str_replace(prednames_fig_1se, "I\\(", "")
prednames_fig_1se <- str_replace(prednames_fig_1se, "\\^2\\)", "")
prednames_fig_1se <- unique(prednames_fig_1se[prednames_fig_1se>0])
prednames_fig_1se_num <- length(prednames_fig_1se)
}
# for 1/2SE lambda model
globModTerms_halfse <- coefs[!is.na(coefs$coefficientValue_halfseLambda), "coefficientName"]
if (length(globModTerms_halfse) == 1) {
prednames_fig_halfse <- paste(str_split(globModTerms_halfse, ":", simplify = TRUE)) 
prednames_fig_halfse <- str_replace(prednames_fig_halfse, "I\\(", "")
prednames_fig_halfse <- str_replace(prednames_fig_halfse, "\\^2\\)", "")
prednames_fig_halfse <- unique(prednames_fig_halfse[prednames_fig_halfse>0])
prednames_fig_halfse_num <- c(0)
} else {
prednames_fig_halfse <- paste(str_split(globModTerms_halfse, ":", simplify = TRUE)) 
prednames_fig_halfse <- str_replace(prednames_fig_halfse, "I\\(", "")
prednames_fig_halfse <- str_replace(prednames_fig_halfse, "\\^2\\)", "")
prednames_fig_halfse <- unique(prednames_fig_halfse[prednames_fig_halfse>0])
prednames_fig_halfse_num <- length(prednames_fig_halfse)
}
# make a table
kable(coefs, col.names = c("Coefficient Name", "Value from best lambda model", 
                           "Value form 1/2 se lambda", "Value from 1se lambda model")
      ) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed")) 
Coefficient Name Value from best lambda model Value form 1/2 se lambda Value from 1se lambda model
(Intercept) -1.4224321 -1.5429724 -1.1614343
tmean 0.4671627 0.6204106 0.1361017
prcp 0.1367873 0.1397180 0.1694032
prcp_dry 0.1034249 0.0002438 0.2893085
isothermality -0.0980145 -0.0857124 NA
annWatDef -0.7179072 -1.2058752 NA
clay -0.2230610 NA NA
sand -0.1761783 NA NA
carbon 0.0619790 0.0433560 NA
AWHC 0.0396783 -0.0215268 NA
prcp_anom -0.2921498 NA -0.2710043
prcpTempCorr_anom -0.1785064 NA NA
isothermality_anom 0.1183581 NA 0.0897515
I(prcpTempCorr^2) 0.0146740 NA NA
I(isothermality^2) -0.0016253 0.0309882 NA
I(prcp_anom^2) 0.0523924 NA NA
I(prcpTempCorr_anom^2) 0.0176093 NA NA
I(annWatDef_anom^2) -0.0019903 NA NA
I(clay^2) -0.0741457 -0.1089390 -0.0584489
I(AWHC^2) -0.0659279 -0.0153778 NA
isothermality:annWatDef_anom -0.0604465 NA NA
isothermality_anom:annWatDef_anom -0.0104978 NA NA
prcp_anom:annWatDef_anom 0.0649058 NA NA
annWatDef_anom:prcpTempCorr -0.0553714 NA NA
tmean:annWatDef_anom 0.0471851 NA NA
isothermality:isothermality_anom -0.0512223 NA NA
isothermality:prcp_anom 0.1210074 NA NA
isothermality_anom:prcpTempCorr -0.1913604 NA -0.1928816
prcp:prcpTempCorr_anom 0.0866102 NA NA
prcp_dry:prcp_anom 0.0773757 NA NA
prcp_anom:prcpTempCorr 0.0745862 NA NA
prcp_dry:prcpTempCorr 0.1866889 0.2550800 0.1701690
prcpTempCorr_anom:prcpTempCorr 0.0942530 NA NA
tmean:prcpTempCorr -0.2692387 -0.3851993 -0.2919240
carbon:AWHC 0.0147280 NA NA
clay:AWHC -0.0144774 NA NA
carbon:coarse 0.0494914 0.0554155 NA
sand:carbon 0.1015367 NA NA
prcpTempCorr NA -0.3324942 NA
prcp:isothermality NA -0.1106833 NA
AWHC:clay NA -0.0654572 NA
carbon:clay NA 0.0017996 NA
carbon:sand NA 0.0692189 NA
prcp:prcp_anom NA NA -0.0497054
tmean:prcp_dry NA NA 0.0511465
clay:carbon NA NA -0.1314337
# calculate RMSE of all models 
RMSE_best <- yardstick::rmse(fullModOut$modelPredictions[,c("obs", "pred_opt")], truth = "obs", estimate = "pred_opt")$.estimate
RMSE_halfse <- yardstick::rmse(fullModOut$modelPredictions[,c("obs", "pred_opt_halfse")], truth = "obs", estimate = "pred_opt_halfse")$.estimate
RMSE_1se <- yardstick::rmse(fullModOut$modelPredictions[,c("obs", "pred_opt_se")], truth = "obs", estimate = "pred_opt_se")$.estimate
# calculate bias of all models
bias_best <-  mean((fullModOut$modelPredictions$obs) - fullModOut$modelPredictions$pred_opt)
bias_halfse <-  mean((fullModOut$modelPredictions$obs) - fullModOut$modelPredictions$pred_opt_halfse)
bias_1se <- mean((fullModOut$modelPredictions$obs) - fullModOut$modelPredictions$pred_opt_se)

uniqueCoeffs <- data.frame("Best lambda model" = c(RMSE_best, bias_best,
  as.integer(length(globModTerms)-1), as.integer(prednames_fig_num), 
                                                   as.integer(sum(prednames_fig %in% c(prednames_clim))),
                                                   as.integer(sum(prednames_fig %in% c(prednames_weath))),
                                                   as.integer(sum(prednames_fig %in% c(prednames_soils)))
                                                   ), 
                           "1/2 se lambda model" = c(RMSE_halfse, bias_halfse,
                             length(globModTerms_halfse)-1, prednames_fig_halfse_num,
                                                   sum(prednames_fig_halfse %in% c(prednames_clim)),
                                                   sum(prednames_fig_halfse %in% c(prednames_weath)),
                                                   sum(prednames_fig_halfse %in% c(prednames_soils))), 
                           "1se lambda model" = c(RMSE_1se, bias_1se,
                             length(globModTerms_1se)-1, prednames_fig_1se_num,
                                                   sum(prednames_fig_1se %in% c(prednames_clim)),
                                                   sum(prednames_fig_1se %in% c(prednames_weath)),
                                                   sum(prednames_fig_1se %in% c(prednames_soils))))
row.names(uniqueCoeffs) <- c("RMSE", "bias: mean(obs-pred.)", "Total number of coefficients", "Number of unique coefficients",
                             "Number of unique climate coefficients", 
                             "Number of unique weather coefficients",  
                             "Number of unique soils coefficients"
                             )

kable(uniqueCoeffs, 
      col.names = c("Best lambda model", "1/2 se lambda model", "1se lambda model"), row.names = TRUE) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed")) 
Best lambda model 1/2 se lambda model 1se lambda model
RMSE 0.2337017 0.2497916 0.2414299
bias: mean(obs-pred.) 0.0000000 0.0000000 0.0000000
Total number of coefficients 37.0000000 18.0000000 12.0000000
Number of unique coefficients 15.0000000 11.0000000 8.0000000
Number of unique climate coefficients 6.0000000 6.0000000 4.0000000
Number of unique weather coefficients 4.0000000 0.0000000 2.0000000
Number of unique soils coefficients 5.0000000 5.0000000 2.0000000

Visualizations of Model Predictions and Residuals – using best lambda model

observed vs. predicted values

If the 1se lambda has no terms (is an intercept only model), use the 1/2 se lambda in subsequent figures

if (length(prednames_fig_1se) == 0) {
  mod_secondBest <- fit_glm_halfse
  name_secondBestMod <- "1/2 SE Model"
  prednames_secondBestMod <- prednames_fig_halfse
} else {
  mod_secondBest <- fit_glm_se
  name_secondBestMod <- "1 SE Model"
  prednames_secondBestMod <- prednames_fig_1se
}

Predicting on the data

  # create prediction for each each model
# (i.e. for each fire proporation variable)
predict_by_response <- function(mod, df) {
  df_out <- df
  response_name <- paste0(response, "_pred")
  preds <- predict(mod, newx= df_out, #s="lambda.min", 
                                     type = "response")
  preds[preds<0] <- 0
  #preds[preds>100] <- 100
  df_out <- df_out %>% cbind(preds)
   colnames(df_out)[ncol(df_out)] <- response_name
  return(df_out)
}

pred_glm1 <- predict_by_response(fit_glm_bestLambda, X[,2:ncol(X)])

## back-transform the 
# add back in true y values
pred_glm1 <- pred_glm1 %>% 
  cbind(modDat_1_s[,c(response, response_t)])

# add back in lat/long data 
pred_glm1 <- pred_glm1 %>% 
  cbind(modDat_1_s[,c("Long", "Lat", "Year")])

pred_glm1$resid <- pred_glm1[,response] - pred_glm1[,paste0(response, "_pred")]
pred_glm1$extremeResid <- NA
pred_glm1[pred_glm1$resid > 1 | pred_glm1$resid < 1,"extremeResid"] <- 1
pred_glm1_1se <- predict_by_response(mod_secondBest, X[,2:ncol(X)])

# add back in true y values
pred_glm1_1se <- pred_glm1_1se %>% 
  cbind(modDat_1_s[,c(response, response_t)])

# add back in lat/long data 
pred_glm1_1se <- pred_glm1_1se %>% 
  cbind(modDat_1_s[,c("Long", "Lat", "Year")])

pred_glm1_1se$resid <- pred_glm1_1se[,response] - pred_glm1_1se[,paste0(response, "_pred")]
pred_glm1_1se$extremeResid <- NA
pred_glm1_1se[pred_glm1_1se$resid > 1 | pred_glm1_1se$resid < -1,"extremeResid"] <- 1

Maps of Observations, Predictions, and Residuals=

Observations across the temporal range of the dataset

pred_glm1 <- pred_glm1 %>% 
  mutate(resid = .[[response]] - .[[paste0(response,"_pred")]]) 

# rasterize
# get reference raster
test_rast <-  rast("../../../Data_raw/dayMet/rawMonthlyData/orders/70e0da02b9d2d6e8faa8c97d211f3546/Daymet_Monthly_V4R1/data/daymet_v4_prcp_monttl_na_1980.tif") %>% 
  terra::aggregate(fact = 8, fun = "mean")
## |---------|---------|---------|---------|=========================================                                          
## add ecoregion boundaries (for our ecoregion level model)
regions <- sf::st_read(dsn = "../../../Data_raw/Level2Ecoregions/", layer = "NA_CEC_Eco_Level2") 
## Reading layer `NA_CEC_Eco_Level2' from data source 
##   `/Users/astears/Documents/Dropbox_static/Work/NAU_USGS_postdoc/cleanPED/PED_vegClimModels/Data_raw/Level2Ecoregions' using driver `ESRI Shapefile'
## Simple feature collection with 2261 features and 8 fields
## Geometry type: POLYGON
## Dimension:     XY
## Bounding box:  xmin: -4334052 ymin: -3313739 xmax: 3324076 ymax: 4267265
## Projected CRS: Sphere_ARC_INFO_Lambert_Azimuthal_Equal_Area
regions <- regions %>% 
  st_transform(crs = st_crs(test_rast)) %>% 
  st_make_valid() 

ecoregionLU <- data.frame("NA_L1NAME" = sort(unique(regions$NA_L1NAME)), 
                        "newRegion" = c(NA, "Forest", "dryShrubGrass", 
                                        "dryShrubGrass", "Forest", "dryShrubGrass",
                                       "dryShrubGrass", "Forest", "Forest", 
                                       "dryShrubGrass", "Forest", "Forest", 
                                       "Forest", "Forest", "dryShrubGrass", 
                                       NA
                                        ))
goodRegions <- regions %>% 
  left_join(ecoregionLU)
mapRegions <- goodRegions %>% 
  filter(!is.na(newRegion)) %>% 
  group_by(newRegion) %>% 
  summarise(geometry = sf::st_union(geometry)) %>% 
  ungroup() %>% 
  st_simplify(dTolerance = 1000)
#mapview(mapRegions)
# rasterize data
plotObs <- pred_glm1 %>% 
         drop_na(paste(response)) %>% 
  #slice_sample(n = 5e4) %>%
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) %>% 
  terra::rasterize(y = test_rast, 
                   field = response, 
                   fun = mean) #%>% 
  #terra::aggregate(fact = 2, fun = mean, na.rm = TRUE) %>% 
  #terra::crop(ext(-1950000, 1000000, -1800000, 1000000))

# get the extent of this particular raster, and crop it accordingly
tempExt <- crds(plotObs, na.rm = TRUE)

plotObs_2 <- plotObs %>% 
  crop(ext(min(tempExt[,1]), max(tempExt[,1]),
           min(tempExt[,2]), max(tempExt[,2])) 
       )
# make figures
map_obs <- ggplot() +
geom_spatraster(data = plotObs_2) + 
  geom_sf(data=cropped_states %>% st_transform(crs = st_crs(test_rast)) %>% st_crop(st_bbox(plotObs_2)),fill=NA ) +
  geom_sf(data = mapRegions, fill = NA, col = "orchid", lwd = .5) +
labs(title = paste0("Observations of ", response, " in the ",ecoregion, " ecoregion")) +
  scale_fill_gradient2(low = "brown",
                       mid = "wheat" ,
                       high = "darkgreen" , 
                       midpoint = 0,   na.value = "grey20") + 
  xlim(st_bbox(plotObs_2)[c(1,3)]) + 
  ylim(st_bbox(plotObs_2)[c(2,4)])

hist_obs <- ggplot(pred_glm1) + 
  geom_histogram(aes(.data[[response]]), fill = "lightgrey", col = "darkgrey")

library(ggpubr)
ggarrange(map_obs, hist_obs, heights = c(3,1), ncol = 1)

Predictions across the temporal range of the dataset

# rasterize data
plotPred <- pred_glm1 %>% 
         drop_na(paste0(response,"_pred")) %>% 
  #slice_sample(n = 5e4) %>%
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) %>% 
  terra::rasterize(y = test_rast, 
                   field = paste0(response,"_pred"), 
                   fun = mean) 

# get the point location of those predictions that are > 100
highPred_points <- pred_glm1 %>% 
  filter(.[[paste0(response,"_pred")]] > 100 | 
           .[[paste0(response, "_pred")]] < 0) %>% 
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) 

# get the extent of this particular raster, and crop it accordingly
tempExt <- crds(plotPred, na.rm = TRUE)

plotPred_2 <- plotPred %>% 
  crop(ext(min(tempExt[,1]), max(tempExt[,1]),
           min(tempExt[,2]), max(tempExt[,2])) 
       )
# make figures
map_preds1 <- ggplot() +
geom_spatraster(data = plotPred_2) + 
  geom_sf(data=cropped_states %>% st_transform(crs = st_crs(test_rast)) %>% st_crop(st_bbox(plotObs_2)),fill=NA )  + 
  geom_sf(data = mapRegions, fill = NA, col = "orchid", lwd = .5) +
  geom_sf(data = highPred_points, col = "red") +
labs(title = paste0("Predictions from the 'best lambda' fitted model of ", response, " in the ",ecoregion, " ecoregion"),
     subtitle =  "bestLambda model")  +
  scale_fill_gradient2(low = "wheat",
                       mid = "darkgreen",
                       high = "red" , 
                       midpoint = 1,   na.value = "grey20",
                       limits = c(0,1)) + 
  xlim(st_bbox(plotObs_2)[c(1,3)]) + 
  ylim(st_bbox(plotObs_2)[c(2,4)])

hist_preds1 <- ggplot(pred_glm1) + 
  geom_histogram(aes(.data[[paste0(response, "_pred")]]), fill = "lightgrey", col = "darkgrey")+ 
  xlim(c(0,1))

ggarrange(map_preds1, hist_preds1, heights = c(3,1), ncol = 1)

# rasterize data
plotPred <- pred_glm1_1se %>% 
         drop_na(paste0(response,"_pred")) %>% 
  #slice_sample(n = 5e4) %>%
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) %>% 
  terra::rasterize(y = test_rast, 
                   field = paste0(response,"_pred"), 
                   fun = mean) #%>% 
  #terra::aggregate(fact = 2, fun = mean, na.rm = TRUE) %>% 
  #terra::crop(ext(-1950000, 1000000, -1800000, 1000000))

# get the point location of those predictions that are > 100
highPred_points <- pred_glm1_1se %>% 
  filter(.[[paste0(response,"_pred")]] > 100 | 
           .[[paste0(response, "_pred")]] < 0) %>% 
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) 

# get the extent of this particular raster, and crop it accordingly
tempExt <- crds(plotPred, na.rm = TRUE)

plotPred_2 <- plotPred %>% 
  crop(ext(min(tempExt[,1]), max(tempExt[,1]),
           min(tempExt[,2]), max(tempExt[,2])) 
       )
# make figures
map_preds2 <- ggplot() +
geom_spatraster(data = plotPred_2) + 
  geom_sf(data=cropped_states %>% st_transform(crs = st_crs(test_rast)) %>% st_crop(st_bbox(plotObs_2)),fill=NA )  + 
  geom_sf(data = mapRegions, fill = NA, col = "orchid", lwd = .5) +
  geom_sf(data = highPred_points, col = "red") +
labs(title = paste0("Predictions from the '1SE lambda' fitted model of ", response, " in the ",ecoregion, " ecoregion"),
     subtitle =  name_secondBestMod)  +
  scale_fill_gradient2(low = "wheat",
                       mid = "darkgreen",
                       high = "red" , 
                       midpoint = 1,   na.value = "grey20",
                       limits = c(0, 1)) + 
  xlim(st_bbox(plotObs_2)[c(1,3)]) + 
  ylim(st_bbox(plotObs_2)[c(2,4)])

hist_preds2 <- ggplot(pred_glm1_1se) + 
  geom_histogram(aes(.data[[paste0(response, "_pred")]]), fill = "lightgrey", col = "darkgrey")+ 
  xlim(c(0,1))

ggarrange(map_preds2, hist_preds2, heights = c(3,1), ncol = 1)

Residuals across the entire temporal extent of the dataset

# rasterize data
plotResid_rast <- pred_glm1 %>% 
         drop_na(resid) %>% 
  #slice_sample(n = 5e4) %>%
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) %>% 
  terra::rasterize(y = test_rast, 
                   field = "resid", 
                   fun = mean) #%>% 
  #terra::aggregate(fact = 2, fun = mean, na.rm = TRUE) %>% 
  #terra::crop(ext(-1950000, 1000000, -1800000, 1000000))

# get the extent of this particular raster, and crop it accordingly
tempExt <- crds(plotResid_rast, na.rm = TRUE)

plotResid_rast_2 <- plotResid_rast %>% 
  crop(ext(min(tempExt[,1]), max(tempExt[,1]),
           min(tempExt[,2]), max(tempExt[,2])) 
       )

# identify locations where residuals are >100 or < -100
badResids_high <- pred_glm1 %>% 
  filter(resid > 1)  %>% 
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) 
badResids_low <- pred_glm1 %>% 
  filter(resid < -1)  %>% 
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) 
# make figures
map <- ggplot() +
geom_spatraster(data =plotResid_rast_2) + 
  geom_sf(data=cropped_states %>% st_transform(crs = st_crs(test_rast)) %>% st_crop(st_bbox(plotObs_2)),fill=NA )  + 
  geom_sf(data = mapRegions, fill = NA, col = "orchid", lwd = .5) +
  geom_sf(data = badResids_high, col = "blue") +
  geom_sf(data = badResids_low, col = "red") +
labs(title = paste0("Resids. (obs. - pred.) from the ", ecoregion," ecoregion-wide model of ", response),
     subtitle = "bestLambda model \n red points indicate locations that have residuals below -100 \n blue points indicate locatiosn that have residuals above 100") +
  scale_fill_gradient2(low = "red",
                       mid = "white" ,
                       high = "blue" , 
                       midpoint = 0,   na.value = "grey20",
                       limits = c(-1,1)
                       ) + 
  xlim(st_bbox(plotObs_2)[c(1,3)]) + 
  ylim(st_bbox(plotObs_2)[c(2,4)])
hist <- ggplot(pred_glm1) + 
  geom_histogram(aes(resid), fill = "lightgrey", col = "darkgrey") + 
  geom_text(aes(x = min(resid)*.9, y = 1500, label = paste0("min = ", round(min(resid),2)))) +
  geom_text(aes(x = max(resid)*.9, y = 1500, label = paste0("max = ", round(max(resid),2)))) + 
  geom_vline(aes(xintercept = mean(resid)))

ggarrange(map, hist, heights = c(3,1), ncol = 1)

# rasterize data
plotResid_rast <- pred_glm1_1se %>% 
         drop_na(resid) %>% 
  #slice_sample(n = 5e4) %>%
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) %>% 
  terra::rasterize(y = test_rast, 
                   field = "resid", 
                   fun = mean) #%>% 
  #terra::aggregate(fact = 2, fun = mean, na.rm = TRUE) %>% 
  #terra::crop(ext(-1950000, .700000, -1800000, .700000))

# get the extent of this particular raster, and crop it accordingly
tempExt <- crds(plotResid_rast, na.rm = TRUE)

plotResid_rast_2 <- plotResid_rast %>% 
  crop(ext(min(tempExt[,1]), max(tempExt[,1]),
           min(tempExt[,2]), max(tempExt[,2])) 
       )

# identify locations where residuals are >10 or < -10
badResids_high <- pred_glm1_1se %>% 
  filter(resid > 100)  %>% 
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) 
badResids_low <- pred_glm1_1se %>% 
  filter(resid < -100)  %>% 
  terra::vect(geom = c("Long", "Lat")) %>% 
  terra::set.crs(crs(test_rast)) 
# make figures
map <- ggplot() +
geom_spatraster(data =plotResid_rast_2) + 
  geom_sf(data=cropped_states %>% st_transform(crs = st_crs(test_rast)) %>% st_crop(st_bbox(plotObs_2)),fill=NA )  + 
  geom_sf(data = mapRegions, fill = NA, col = "orchid", lwd = .5) +
  geom_sf(data = badResids_high, col = "blue") +
  geom_sf(data = badResids_low, col = "red") +
labs(title = paste0("Resids. (obs. - pred.) from the ", ecoregion," ecoregion-wide model of ", response),
     subtitle = paste0(name_secondBestMod,"\n red points indicate locations that have residuals below -1 \n blue points indicate locatiosn that have residuals above 1")) +
  scale_fill_gradient2(low = "red",
                       mid = "white" ,
                       high = "blue" , 
                       midpoint = 0,   na.value = "grey20",
                       limits = c(-1,1)
                       ) + 
  xlim(st_bbox(plotObs_2)[c(1,3)]) + 
  ylim(st_bbox(plotObs_2)[c(2,4)])
hist <- ggplot(pred_glm1_1se) + 
  geom_histogram(aes(resid), fill = "lightgrey", col = "darkgrey") + 
  geom_text(aes(x = min(resid)*.9, y = 1500, label = paste0("min = ", round(min(resid),2)))) +
  geom_text(aes(x = max(resid)*.9, y = 1500, label = paste0("max = ", round(max(resid),2))))+ 
  geom_vline(aes(xintercept = mean(resid)))

ggarrange(map, hist, heights = c(3,1), ncol = 1)

Are there biases of the model predictions across year/lat/long?

# plot residuals against Year
yearResidMod_bestLambda <- ggplot(pred_glm1) + 
  geom_point(aes(x = jitter(Year), y = resid), alpha = .1) + 
  geom_smooth(aes(x = Year, y = resid)) + 
  xlab("Year") + 
  ylab("Residuals") +
  ggtitle("from best lamba model")
yearResidMod_1seLambda <- ggplot(pred_glm1_1se) + 
  geom_point(aes(x = jitter(Year), y = resid), alpha = .1) + 
  geom_smooth(aes(x = Year, y = resid)) + 
  xlab("Year") + 
  ylab("Residuals") +
  ggtitle(paste0("from ", name_secondBestMod))

# plot residuals against Lat
latResidMod_bestLambda <- ggplot(pred_glm1) + 
  geom_point(aes(x = Lat, y = resid), alpha = .1) + 
  geom_smooth(aes(x = Lat, y = resid)) + 
  xlab("Latitude") + 
  ylab("Residuals") +
  ggtitle("from best lamba model")
latResidMod_1seLambda <- ggplot(pred_glm1_1se) + 
  geom_point(aes(x = Lat, y = resid), alpha = .1) + 
  geom_smooth(aes(x = Lat, y = resid)) + 
  xlab("Latitude") + 
  ylab("Residuals") +
  ggtitle(paste0("from ", name_secondBestMod))

# plot residuals against Long
longResidMod_bestLambda <- ggplot(pred_glm1) + 
  geom_point(aes(x = Long, y = resid), alpha = .1) + 
  geom_smooth(aes(x = Long, y = resid)) + 
  xlab("Longitude") + 
  ylab("Residuals") +
  ggtitle("from best lamba model")
longResidMod_1seLambda <- ggplot(pred_glm1_1se) + 
  geom_point(aes(x = Long, y = resid), alpha = .1) + 
  geom_smooth(aes(x = Long, y = resid)) + 
  xlab("Longitude") + 
  ylab("Residuals") +
  ggtitle(paste0("from ", name_secondBestMod))

library(patchwork)
(yearResidMod_bestLambda + yearResidMod_1seLambda) / 
(  latResidMod_bestLambda + latResidMod_1seLambda) /
(  longResidMod_bestLambda + longResidMod_1seLambda)

Quantile plots

Binning predictor variables into “Quantiles” and looking at the mean predicted probability for each percentile.

# get deciles for best lambda model 
if (length(prednames_fig) == 0) {
  print("The best lambda model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {
  pred_glm1_deciles <- predvars2deciles(pred_glm1,
                                      response_vars = response_vars,
                                        pred_vars = prednames_fig, 
                                       cut_points = seq(0, 1, 0.005))
}
# get deciles for 1 SE lambda model 
if (length(prednames_secondBestMod) == 0) {
  print("The 1SE (or 1/2 SE) lambda model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {
  pred_glm1_deciles_1se <- predvars2deciles(pred_glm1_1se,
                                      response_vars = response_vars,
                                        pred_vars = prednames_secondBestMod, 
                                       cut_points = seq(0, 1, 0.005))
}

Below are quantile plots for the best lambda model (note that the predictor variables are scaled)

if (length(prednames_fig) == 0) {
  print("The model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {

# publication quality version
g3 <- decile_dotplot_pq(df = pred_glm1_deciles, response = c(response, paste0(response, "_pred")), IQR = TRUE,
                        CI = FALSE
                        ) + ggtitle("Decile Plot")

g4 <- add_dotplot_inset(g3, df = pred_glm1_deciles, response = c(response, paste0(response, "_pred")), dfRaw = pred_glm1, add_smooth = TRUE, deciles = FALSE)

  
if(save_figs) {
  png(paste0("figures/quantile_plots/quantile_plot_", response,  "_",ecoregion,".png"), 
     units = "in", res = 600, width = 5.5, height = 3.5 )
    print(g4)
  dev.off()
}

g4
}

Below are percentile plots from the second best lambda model ()

# get prednames for the second best SE lambda model
if(name_secondBestMod == "1 SE Model") {
  
} else {
  
}
## NULL
if (length(prednames_secondBestMod) == 0) {
  print("The 1 se lambda model only contains one predictor (an intercept), so decile plots aren't possible to generate")

  } else {

# publication quality version
g3 <- decile_dotplot_pq(pred_glm1_deciles_1se, response = c(response, paste0(response, "_pred")), IQR = TRUE) + ggtitle("Decile Plot")

g4 <- add_dotplot_inset(g3, df = pred_glm1_deciles_1se, response = c(response, paste0(response, "_pred")), dfRaw = pred_glm1_1se, add_smooth = TRUE, deciles = FALSE)

  
if(save_figs) {
  png(paste0("figures/quantile_plots/quantile_plot_", response,  "_",ecoregion,".png"), 
     units = "in", res = 600, width = 5.5, height = 3.5 )
    print(g4)
  dev.off()
}

g4
}

Filtered Quantiles

For the best lambda model

df <- pred_glm1[, prednames_fig] #%>% 
  #mutate(MAT = MAT - 273.15) # k to c
quantiles <- purrr::map(df, quantile, probs = c(0.2, 0.8), na.rm = TRUE)

Filtered ‘Quantile’ plots of data. These plots show each vegetation variable, but only based on data that falls into the upper and lower 20th percentiles of each predictor variable.

if (length(prednames_fig) == 0) {
  print("The model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {
pred_glm1_deciles_filt <- predvars2deciles( pred_glm1, 
                         response_vars = c(response, paste0(response, "_pred")),
                         pred_vars = prednames_fig,
                         filter_var = TRUE,
                         filter_vars = prednames_fig,
                         cut_points = seq(0, 1, 0.005)) 
g <- decile_dotplot_filtered_pq(df = pred_glm1_deciles_filt, response = response, 
                                xvars = prednames_fig)

if(save_figs) {x
jpeg(paste0("figures/quantile_plots/quantile_plot_filtered_mid_v1", , ".jpeg"),
     units = "in", res = 600, width = 5.5, height = 6 )
  g 
dev.off()
}
g
}
## Processed 12540 groups out of 89487. 14% done. Time elapsed: 3s. ETA: 18s.Processed 16268 groups out of 89487. 18% done. Time elapsed: 4s. ETA: 18s.Processed 21134 groups out of 89487. 24% done. Time elapsed: 5s. ETA: 16s.Processed 26046 groups out of 89487. 29% done. Time elapsed: 6s. ETA: 14s.Processed 31017 groups out of 89487. 35% done. Time elapsed: 7s. ETA: 13s.Processed 35991 groups out of 89487. 40% done. Time elapsed: 8s. ETA: 11s.Processed 40807 groups out of 89487. 46% done. Time elapsed: 9s. ETA: 10s.Processed 45754 groups out of 89487. 51% done. Time elapsed: 10s. ETA: 9s.Processed 50711 groups out of 89487. 57% done. Time elapsed: 11s. ETA: 8s.Processed 55642 groups out of 89487. 62% done. Time elapsed: 12s. ETA: 7s.Processed 60556 groups out of 89487. 68% done. Time elapsed: 13s. ETA: 6s.Processed 65501 groups out of 89487. 73% done. Time elapsed: 14s. ETA: 5s.Processed 70447 groups out of 89487. 79% done. Time elapsed: 15s. ETA: 4s.Processed 75356 groups out of 89487. 84% done. Time elapsed: 16s. ETA: 3s.Processed 80070 groups out of 89487. 89% done. Time elapsed: 17s. ETA: 1s.Processed 84774 groups out of 89487. 95% done. Time elapsed: 18s. ETA: 1s.Processed 89412 groups out of 89487. 100% done. Time elapsed: 19s. ETA: 0s.Processed 89487 groups out of 89487. 100% done. Time elapsed: 19s. ETA: 0s.

Filtered quantile figure with middle 2 deciles also shown

if (length(prednames_fig) == 0) {
  print("The model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {
pred_glm1_deciles_filt_mid <- predvars2deciles(pred_glm1, 
                         response_vars = c(response, paste0(response, "_pred")),
                         pred_vars = prednames_fig,
                         filter_vars = prednames_fig,
                         filter_var = TRUE,
                         add_mid = TRUE,
                         cut_points = seq(0, 1, 0.005))

g <- decile_dotplot_filtered_pq(df = pred_glm1_deciles_filt_mid, response = response, 
                                xvars = prednames_fig)


if(save_figs) {x
jpeg(paste0("figures/quantile_plots/quantile_plot_filtered_mid_v1", , ".jpeg"),
     units = "in", res = 600, width = 5.5, height = 6 )
  g 
dev.off()
}
g
}
## Processed 12505 groups out of 134362. 9% done. Time elapsed: 3s. ETA: 29s.Processed 17193 groups out of 134362. 13% done. Time elapsed: 4s. ETA: 27s.Processed 21879 groups out of 134362. 16% done. Time elapsed: 5s. ETA: 25s.Processed 26544 groups out of 134362. 20% done. Time elapsed: 6s. ETA: 24s.Processed 31323 groups out of 134362. 23% done. Time elapsed: 7s. ETA: 23s.Processed 36020 groups out of 134362. 27% done. Time elapsed: 8s. ETA: 21s.Processed 40833 groups out of 134362. 30% done. Time elapsed: 9s. ETA: 20s.Processed 45654 groups out of 134362. 34% done. Time elapsed: 10s. ETA: 19s.Processed 50332 groups out of 134362. 37% done. Time elapsed: 11s. ETA: 18s.Processed 54809 groups out of 134362. 41% done. Time elapsed: 12s. ETA: 17s.Processed 59522 groups out of 134362. 44% done. Time elapsed: 13s. ETA: 16s.Processed 64126 groups out of 134362. 48% done. Time elapsed: 14s. ETA: 15s.Processed 68884 groups out of 134362. 51% done. Time elapsed: 15s. ETA: 14s.Processed 73671 groups out of 134362. 55% done. Time elapsed: 16s. ETA: 13s.Processed 78381 groups out of 134362. 58% done. Time elapsed: 17s. ETA: 12s.Processed 83083 groups out of 134362. 62% done. Time elapsed: 18s. ETA: 11s.Processed 87864 groups out of 134362. 65% done. Time elapsed: 19s. ETA: 10s.Processed 92729 groups out of 134362. 69% done. Time elapsed: 20s. ETA: 8s.Processed 97451 groups out of 134362. 73% done. Time elapsed: 21s. ETA: 7s.Processed 102261 groups out of 134362. 76% done. Time elapsed: 22s. ETA: 6s.Processed 107124 groups out of 134362. 80% done. Time elapsed: 23s. ETA: 5s.Processed 111754 groups out of 134362. 83% done. Time elapsed: 24s. ETA: 4s.Processed 116401 groups out of 134362. 87% done. Time elapsed: 25s. ETA: 3s.Processed 121230 groups out of 134362. 90% done. Time elapsed: 26s. ETA: 2s.Processed 125912 groups out of 134362. 94% done. Time elapsed: 27s. ETA: 1s.Processed 130614 groups out of 134362. 97% done. Time elapsed: 28s. ETA: 0s.Processed 134362 groups out of 134362. 100% done. Time elapsed: 28s. ETA: 0s.

For the second best lambda model ()

df <- pred_glm1_1se[, prednames_secondBestMod] #%>% 
  #mutate(MAT = MAT - 273.15) # k to c
quantiles <- purrr::map(df, quantile, probs = c(0.2, 0.8), na.rm = TRUE)

Filtered ‘Quantile’ plots of data. These plots show each vegetation variable, but only based on data that falls into the upper and lower 20th percentiles of each predictor variable.

if (length(prednames_secondBestMod) == 0) {
  print("The model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {
  
pred_glm1_deciles_filt <- predvars2deciles( pred_glm1_1se, 
                         response_vars = c(response, paste0(response, "_pred")),
                         pred_vars = prednames_secondBestMod,
                         filter_var = TRUE,
                         filter_vars = prednames_secondBestMod,
                         cut_points = seq(0, 1, 0.005)) 
g <- decile_dotplot_filtered_pq(df = pred_glm1_deciles_filt, response = response, 
                                xvars = prednames_fig)

if(save_figs) {
jpeg(paste0("figures/quantile_plots/quantile_plot_filtered_mid_v1", , ".jpeg"),
     units = "in", res = 600, width = 5.5, height = 6 )
  g 
dev.off()
}
g
}
## Processed 9063 groups out of 25553. 35% done. Time elapsed: 3s. ETA: 5s.Processed 13550 groups out of 25553. 53% done. Time elapsed: 4s. ETA: 3s.Processed 18440 groups out of 25553. 72% done. Time elapsed: 5s. ETA: 1s.Processed 23204 groups out of 25553. 91% done. Time elapsed: 6s. ETA: 0s.Processed 25553 groups out of 25553. 100% done. Time elapsed: 6s. ETA: 0s.

Filtered quantile figure with middle 2 deciles also shown

if (length(prednames_secondBestMod) == 0) {
  print("The model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {
pred_glm1_deciles_filt_mid <- predvars2deciles(pred_glm1, 
                         response_vars = c(response, paste0(response, "_pred")),
                         pred_vars = prednames_fig,
                         filter_vars = prednames_fig,
                         filter_var = TRUE,
                         add_mid = TRUE,
                         cut_points = seq(0, 1, 0.005))

g <- decile_dotplot_filtered_pq(df = pred_glm1_deciles_filt_mid, response = response, 
                                xvars = prednames_fig)


if(save_figs) {x
jpeg(paste0("figures/quantile_plots/quantile_plot_filtered_mid_v1", , ".jpeg"),
     units = "in", res = 600, width = 5.5, height = 6 )
  g 
dev.off()
}
g
}
## Processed 13447 groups out of 134362. 10% done. Time elapsed: 3s. ETA: 26s.Processed 17889 groups out of 134362. 13% done. Time elapsed: 4s. ETA: 26s.Processed 22268 groups out of 134362. 17% done. Time elapsed: 5s. ETA: 25s.Processed 26920 groups out of 134362. 20% done. Time elapsed: 6s. ETA: 23s.Processed 31380 groups out of 134362. 23% done. Time elapsed: 7s. ETA: 22s.Processed 35874 groups out of 134362. 27% done. Time elapsed: 8s. ETA: 21s.Processed 40273 groups out of 134362. 30% done. Time elapsed: 9s. ETA: 21s.Processed 44899 groups out of 134362. 33% done. Time elapsed: 10s. ETA: 19s.Processed 49617 groups out of 134362. 37% done. Time elapsed: 11s. ETA: 18s.Processed 52919 groups out of 134362. 39% done. Time elapsed: 12s. ETA: 18s.Processed 57662 groups out of 134362. 43% done. Time elapsed: 13s. ETA: 17s.Processed 62490 groups out of 134362. 47% done. Time elapsed: 14s. ETA: 16s.Processed 67164 groups out of 134362. 50% done. Time elapsed: 15s. ETA: 15s.Processed 71895 groups out of 134362. 54% done. Time elapsed: 16s. ETA: 13s.Processed 76664 groups out of 134362. 57% done. Time elapsed: 17s. ETA: 12s.Processed 81389 groups out of 134362. 61% done. Time elapsed: 18s. ETA: 11s.Processed 86231 groups out of 134362. 64% done. Time elapsed: 19s. ETA: 10s.Processed 91105 groups out of 134362. 68% done. Time elapsed: 20s. ETA: 9s.Processed 95840 groups out of 134362. 71% done. Time elapsed: 21s. ETA: 8s.Processed 100633 groups out of 134362. 75% done. Time elapsed: 22s. ETA: 7s.Processed 105197 groups out of 134362. 78% done. Time elapsed: 23s. ETA: 6s.Processed 109904 groups out of 134362. 82% done. Time elapsed: 24s. ETA: 5s.Processed 114678 groups out of 134362. 85% done. Time elapsed: 25s. ETA: 4s.Processed 119563 groups out of 134362. 89% done. Time elapsed: 26s. ETA: 3s.Processed 124310 groups out of 134362. 93% done. Time elapsed: 27s. ETA: 2s.Processed 129218 groups out of 134362. 96% done. Time elapsed: 28s. ETA: 1s.Processed 134091 groups out of 134362. 100% done. Time elapsed: 29s. ETA: 0s.Processed 134362 groups out of 134362. 100% done. Time elapsed: 29s. ETA: 0s.

Show model RMSE w/in each quantile

# get deciles for best lambda model 
if (length(prednames_fig) == 0) {
  print("The best lambda model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {
  pred_glm1_deciles %>% 
    ggplot(aes(x = mean_value, y = RMSE)) +
    facet_wrap(~name, scales = "free_x")+
    geom_point(alpha = .2, size = .5) + 
    geom_smooth(lwd = .5) + 
    xlab("Scaled predictor value") + 
    ggtitle("RMSE by decile for bestLambda model")
}

# get deciles for 1 SE lambda model 
if (length(prednames_secondBestMod) == 0) {
  print("The 1SE (or 1/2 SE) lambda model only contains one predictor (an intercept), so decile plots aren't possible to generate")
} else {
  pred_glm1_deciles_1se %>% 
    ggplot(aes(x = mean_value, y = RMSE)) +
    facet_wrap(~name, scales = "free_x")+
    geom_point(alpha = .2, size = .5) + 
    geom_smooth(lwd = .5) + 
    xlab("Scaled predictor value") + 
    ggtitle(paste0("RMSE by decile for ", name_secondBestMod, "model"))
}